Project ID: plumID:25.019
Source: templates/template_Chignolin_OneOPES/4/plumed.dat
Originally used with PLUMED version: 2.9.1
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes
tested onv2.10
tested onmaster
#RESTART
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=protein STRUCTUREa file in pdb format containing a reference structure=folded.pdb
WO: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=167-5885:3
WH: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=168-5886:3,169-5887:3
rmsd_ca: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=foldedCA.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL

# Distance between pairs of atoms of residues 3 and 8
cont_H_46-O_120: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=46 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=120 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_46-N_45: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,45
H-A_H_46-O_120: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,120
H-B_H_46-C_119: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,119
D-A_N_45-O_120: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,120
A-B_O_120-C_119: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=120,119
ang_DHA_hbond_H_46-O_120: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_45-O_120,H-D_H_46-N_45,H-A_H_46-O_120 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_46-O_120: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_46-C_119,H-A_H_46-O_120,A-B_O_120-C_119 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_46-O_120: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_46-O_120,ang_DHA_hbond_H_46-O_120,ang_BAH_hbond_H_46-O_120 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_46-O_120: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=119,120,121 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_46-O_120: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=45,46,47 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_46-O_120: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-O_120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_46-O_120: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-O_120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 10 and 1
cont_H_146-O_23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=146 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_146-N_145: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=146,145
H-A_H_146-O_23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=146,23
H-B_H_146-C_22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=146,22
D-A_N_145-O_23: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=145,23
A-B_O_23-C_22: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=23,22
ang_DHA_hbond_H_146-O_23: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_145-O_23,H-D_H_146-N_145,H-A_H_146-O_23 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_146-O_23: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_146-C_22,H-A_H_146-O_23,A-B_O_23-C_22 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_146-O_23: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_146-O_23,ang_DHA_hbond_H_146-O_23,ang_BAH_hbond_H_146-O_23 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_146-O_23: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=22,23,24 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_146-O_23: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=145,146,147 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_146-O_23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_146-O_23 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_146-O_23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_146-O_23 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 7 and 3
cont_H_101-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=101 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=56 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_101-N_100: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,100
H-A_H_101-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,56
H-B_H_101-C_55: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,55
D-A_N_100-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=100,56
A-B_O_56-C_55: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=56,55
ang_DHA_hbond_H_101-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_100-O_56,H-D_H_101-N_100,H-A_H_101-O_56 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_101-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_101-C_55,H-A_H_101-O_56,A-B_O_56-C_55 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_101-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_101-O_56,ang_DHA_hbond_H_101-O_56,ang_BAH_hbond_H_101-O_56 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_101-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=55,56,57 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_101-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=100,101,102 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_101-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_101-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_101-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_101-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 8 and 3
cont_H_108-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=108 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=56 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_108-N_107: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,107
H-A_H_108-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,56
H-B_H_108-C_55: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,55
D-A_N_107-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=107,56
ang_DHA_hbond_H_108-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_107-O_56,H-D_H_108-N_107,H-A_H_108-O_56 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_108-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_108-C_55,H-A_H_108-O_56,A-B_O_56-C_55 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_108-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_108-O_56,ang_DHA_hbond_H_108-O_56,ang_BAH_hbond_H_108-O_56 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_108-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=55,56,57 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_108-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=107,108,109 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_108-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_108-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_108-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_108-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 8 and 6
cont_HG1_114-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=114 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=92 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_HG1_114-OG1_113: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=114,113
H-A_HG1_114-OG1_92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=114,92
H-B_HG1_114-CB_90: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=114,90
D-A_OG1_113-OG1_92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=113,92
A-B_OG1_92-CB_90: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=92,90
ang_DHA_hbond_HG1_114-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_OG1_113-OG1_92,H-D_HG1_114-OG1_113,H-A_HG1_114-OG1_92 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_HG1_114-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_HG1_114-CB_90,H-A_HG1_114-OG1_92,A-B_OG1_92-CB_90 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_HG1_114-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_HG1_114-OG1_92,ang_DHA_hbond_HG1_114-OG1_92,ang_BAH_hbond_HG1_114-OG1_92 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_HG1_114-OG1_92: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=90,92,93 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_HG1_114-OG1_92: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=113,114,115 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_HG1_114-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_114-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_HG1_114-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_114-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_108-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=108 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=92 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_108-OG1_92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,92
H-B_H_108-CB_90: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=108,90
D-A_N_107-OG1_92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=107,92
ang_DHA_hbond_H_108-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_107-OG1_92,H-D_H_108-N_107,H-A_H_108-OG1_92 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_108-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_108-CB_90,H-A_H_108-OG1_92,A-B_OG1_92-CB_90 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_108-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_108-OG1_92,ang_DHA_hbond_H_108-OG1_92,ang_BAH_hbond_H_108-OG1_92 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_108-OG1_92: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=90,92,93 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_108-OG1_92: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=107,108,109 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_108-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_108-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_108-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_108-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 6 and 3
cont_H_87-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=87 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_87-N_86: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,86
H-A_H_87-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,54
H-B_H_87-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,52
D-A_N_86-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=86,54
A-B_OD2_54-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=54,52
ang_DHA_hbond_H_87-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_86-OD2_54,H-D_H_87-N_86,H-A_H_87-OD2_54 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_87-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_87-CG_52,H-A_H_87-OD2_54,A-B_OD2_54-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_87-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-OD2_54,ang_DHA_hbond_H_87-OD2_54,ang_BAH_hbond_H_87-OD2_54 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_87-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,54,55 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_87-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=86,87,88 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_87-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_87-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_87-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=87 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=53 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_87-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,53
D-A_N_86-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=86,53
A-B_OD1_53-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=53,52
ang_DHA_hbond_H_87-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_86-OD1_53,H-D_H_87-N_86,H-A_H_87-OD1_53 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_87-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_87-CG_52,H-A_H_87-OD1_53,A-B_OD1_53-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_87-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-OD1_53,ang_DHA_hbond_H_87-OD1_53,ang_BAH_hbond_H_87-OD1_53 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_87-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,53,54 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_87-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=86,87,88 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_87-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_87-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_HG1_93-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=93 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_HG1_93-OG1_92: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=93,92
H-A_HG1_93-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=93,54
H-B_HG1_93-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=93,52
D-A_OG1_92-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=92,54
ang_DHA_hbond_HG1_93-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_OG1_92-OD2_54,H-D_HG1_93-OG1_92,H-A_HG1_93-OD2_54 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_HG1_93-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_HG1_93-CG_52,H-A_HG1_93-OD2_54,A-B_OD2_54-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_HG1_93-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_HG1_93-OD2_54,ang_DHA_hbond_HG1_93-OD2_54,ang_BAH_hbond_HG1_93-OD2_54 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_HG1_93-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,54,55 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_HG1_93-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=92,93,94 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_HG1_93-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_93-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_HG1_93-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_93-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_HG1_93-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=93 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=53 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_HG1_93-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=93,53
D-A_OG1_92-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=92,53
ang_DHA_hbond_HG1_93-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_OG1_92-OD1_53,H-D_HG1_93-OG1_92,H-A_HG1_93-OD1_53 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_HG1_93-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_HG1_93-CG_52,H-A_HG1_93-OD1_53,A-B_OD1_53-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_HG1_93-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_HG1_93-OD1_53,ang_DHA_hbond_HG1_93-OD1_53,ang_BAH_hbond_HG1_93-OD1_53 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_HG1_93-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,53,54 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_HG1_93-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=92,93,94 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_HG1_93-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_93-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_HG1_93-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_93-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 5 and 3
cont_H_72-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=72 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_72-N_71: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=72,71
H-A_H_72-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=72,54
H-B_H_72-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=72,52
D-A_N_71-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=71,54
ang_DHA_hbond_H_72-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_71-OD2_54,H-D_H_72-N_71,H-A_H_72-OD2_54 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_72-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_72-CG_52,H-A_H_72-OD2_54,A-B_OD2_54-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_72-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_72-OD2_54,ang_DHA_hbond_H_72-OD2_54,ang_BAH_hbond_H_72-OD2_54 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_72-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,54,55 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_72-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=71,72,73 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_72-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_72-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_72-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_72-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_72-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=72 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=53 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_72-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=72,53
D-A_N_71-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=71,53
ang_DHA_hbond_H_72-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_71-OD1_53,H-D_H_72-N_71,H-A_H_72-OD1_53 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_72-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_72-CG_52,H-A_H_72-OD1_53,A-B_OD1_53-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_72-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_72-OD1_53,ang_DHA_hbond_H_72-OD1_53,ang_BAH_hbond_H_72-OD1_53 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_72-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,53,54 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_72-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=71,72,73 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_72-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_72-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_72-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_72-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 1 and 10
cont_H2_3-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=165 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H2_3-N_1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,1
H-A_H2_3-O_165: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,165
H-B_H2_3-C_164: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,164
D-A_N_1-O_165: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,165
A-B_O_165-C_164: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=165,164
ang_DHA_hbond_H2_3-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_1-O_165,H-D_H2_3-N_1,H-A_H2_3-O_165 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H2_3-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H2_3-C_164,H-A_H2_3-O_165,A-B_O_165-C_164 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H2_3-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H2_3-O_165,ang_DHA_hbond_H2_3-O_165,ang_BAH_hbond_H2_3-O_165 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H2_3-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=164,165,166 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H2_3-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,3,4 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H2_3-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H2_3-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H2_3-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H2_3-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H3_4-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=165 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H3_4-N_1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,1
H-A_H3_4-O_165: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,165
H-B_H3_4-C_164: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,164
ang_DHA_hbond_H3_4-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_1-O_165,H-D_H3_4-N_1,H-A_H3_4-O_165 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H3_4-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H3_4-C_164,H-A_H3_4-O_165,A-B_O_165-C_164 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H3_4-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H3_4-O_165,ang_DHA_hbond_H3_4-O_165,ang_BAH_hbond_H3_4-O_165 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H3_4-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=164,165,166 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H3_4-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,4,5 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H3_4-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H3_4-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H3_4-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H3_4-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_2-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=165 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-D_H_2-N_1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,1
H-A_H_2-O_165: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,165
H-B_H_2-C_164: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,164
ang_DHA_hbond_H_2-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_1-O_165,H-D_H_2-N_1,H-A_H_2-O_165 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_2-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_2-C_164,H-A_H_2-O_165,A-B_O_165-C_164 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_2-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_2-O_165,ang_DHA_hbond_H_2-O_165,ang_BAH_hbond_H_2-O_165 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_2-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=164,165,166 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_2-O_165: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,2,3 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_2-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_2-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_2-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_2-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H2_3-OXT_166: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=166 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H2_3-OXT_166: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,166
D-A_N_1-OXT_166: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,166
A-B_OXT_166-C_164: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=166,164
ang_DHA_hbond_H2_3-OXT_166: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_1-OXT_166,H-D_H2_3-N_1,H-A_H2_3-OXT_166 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H2_3-OXT_166: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H2_3-C_164,H-A_H2_3-OXT_166,A-B_OXT_166-C_164 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H2_3-OXT_166: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H2_3-OXT_166,ang_DHA_hbond_H2_3-OXT_166,ang_BAH_hbond_H2_3-OXT_166 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H2_3-OXT_166: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=164,166,167 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H2_3-OXT_166: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,3,4 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H2_3-OXT_166: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H2_3-OXT_166 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H2_3-OXT_166: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H2_3-OXT_166 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 7 and 4
cont_H_101-O_70: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=101 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=70 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_101-O_70: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,70
H-B_H_101-C_69: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=101,69
D-A_N_100-O_70: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=100,70
A-B_O_70-C_69: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=70,69
ang_DHA_hbond_H_101-O_70: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_100-O_70,H-D_H_101-N_100,H-A_H_101-O_70 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_101-O_70: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_101-C_69,H-A_H_101-O_70,A-B_O_70-C_69 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_101-O_70: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_101-O_70,ang_DHA_hbond_H_101-O_70,ang_BAH_hbond_H_101-O_70 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_101-O_70: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=69,70,71 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_101-O_70: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=100,101,102 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_101-O_70: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_101-O_70 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_101-O_70: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_101-O_70 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_87-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=87 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=56 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_87-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,56
H-B_H_87-C_55: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=87,55
D-A_N_86-O_56: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=86,56
ang_DHA_hbond_H_87-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_86-O_56,H-D_H_87-N_86,H-A_H_87-O_56 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_87-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_87-C_55,H-A_H_87-O_56,A-B_O_56-C_55 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_87-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-O_56,ang_DHA_hbond_H_87-O_56,ang_BAH_hbond_H_87-O_56 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_87-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=55,56,57 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_87-O_56: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=86,87,88 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_87-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_87-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Distance between pairs of atoms of residues 3 and 3
cont_H_46-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=46 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=53 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_46-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,53
H-B_H_46-CG_52: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,52
D-A_N_45-OD1_53: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,53
ang_DHA_hbond_H_46-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_45-OD1_53,H-D_H_46-N_45,H-A_H_46-OD1_53 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_46-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_46-CG_52,H-A_H_46-OD1_53,A-B_OD1_53-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_46-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_46-OD1_53,ang_DHA_hbond_H_46-OD1_53,ang_BAH_hbond_H_46-OD1_53 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_46-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,53,54 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_46-OD1_53: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=45,46,47 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_46-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_46-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
cont_H_46-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=46 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54 SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8}
H-A_H_46-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=46,54
D-A_N_45-OD2_54: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=45,54
ang_DHA_hbond_H_46-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D-A_N_45-OD2_54,H-D_H_46-N_45,H-A_H_46-OD2_54 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
ang_BAH_hbond_H_46-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=H-B_H_46-CG_52,H-A_H_46-OD2_54,A-B_OD2_54-CG_52 FUNCthe function you wish to evaluate=x/(y+z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
hbond_H_46-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_46-OD2_54,ang_DHA_hbond_H_46-OD2_54,ang_BAH_hbond_H_46-OD2_54 FUNCthe function you wish to evaluate=x*y*z PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
VA_H_46-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=52,54,55 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
VH_H_46-OD2_54: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=45,46,47 COORDINATEScoordinates of the ghost atom in the local reference frame=0.25,0.0,0.0
NWH_H_46-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_H_46-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_101-O_70: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_101-O_70 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=107,45,85,99,120,106,37,44,113,121,82,83,24,158,23,145,131,144,16,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_101-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_101-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=107,45,85,99,120,106,37,44,113,121,82,83,24,158,23,145,131,144,16,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_146-O_23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_146-O_23 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=165,166,45,121,144,44,131,107,56,106,113,57,158,16,53,54,92,37,100,71,86,99,70,85,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_2-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_2-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23,24,145,144,44,120,45,121,16,131,107,56,158,57,106,113,53,54,37,92,100,71,86,99,70,85,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_72-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_72-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=86,45,70,44,92,82,83,100,85,107,120,99,113,24,16,37,106,158,23,121,145,1,144,131,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_72-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_72-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=86,45,70,44,92,82,83,100,85,107,120,99,113,24,16,37,106,158,23,121,145,1,144,131,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H3_4-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H3_4-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23,24,145,144,44,120,45,121,16,131,107,158,56,57,53,54,113,106,37,92,100,71,86,99,70,85,83,82, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_HG1_93-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_93-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=56,71,100,57,45,113,85,107,99,158,120,70,82,83,44,106,121,24,23,37,145,16,144,1,131,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_HG1_93-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_93-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=56,71,100,57,45,113,85,107,99,158,120,70,82,83,44,106,121,24,23,37,145,16,144,1,131,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_108-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_108-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=57,71,106,85,121,70,44,158,37,24,23,145,144,82,83,131,16,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_108-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_108-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=57,71,106,85,121,70,44,158,37,24,23,145,144,82,83,131,16,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_46-O_120: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-O_120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23,145,106,24,113,44,100,144,92,57,54,53,131,37,158,86,99,71,1,165,166,70,85,16,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_46-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23,145,106,24,113,44,100,144,92,57,54,53,131,37,158,86,99,71,1,165,166,70,85,16,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_46-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=23,145,106,24,113,44,100,144,92,57,54,53,131,37,158,86,99,71,1,165,166,70,85,16,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_87-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=45,85,70,107,99,113,120,44,82,83,106,158,121,37,24,23,16,145,144,131,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_87-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=45,85,70,107,99,113,120,44,82,83,106,158,121,37,24,23,16,145,144,131,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H_87-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_87-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=45,85,70,107,99,113,120,44,82,83,106,158,121,37,24,23,16,145,144,131,1,165,166, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_HG1_114-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_HG1_114-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54,53,56,120,158,106,85,45,121,71,57,70,144,145,44,37,82,83,23,24,131,165,166,16,1, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H2_3-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H2_3-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=145,24,144,44,120,121,45,16,131,107,158,56,57,113,106,53,54,37,92,100,71,86,99,70,85,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_H2_3-OXT_166: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H2_3-OXT_166 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=145,24,144,44,120,121,45,16,131,107,158,56,57,113,106,53,54,37,92,100,71,86,99,70,85,82,83, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_87-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,96,95,97,101,80,79,108,91,74,60,89,46,112,67,114,62,159,68,64,103,163,65,156,27,104,110,116,118,17,117,161,154,14,33,25,40,21,30,150,35,124,42,12,146,19,122,9,38,29,151,8,6,148,126,130,3,4,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_46-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,96,95,97,101,80,79,108,91,74,60,89,46,112,67,114,62,159,68,64,103,163,65,156,27,104,110,116,118,17,117,161,154,14,33,25,40,21,30,150,35,124,42,12,146,19,122,9,38,29,151,8,6,148,126,130,3,4,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_HG1_93-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_93-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,96,95,97,101,80,79,108,91,74,60,89,46,112,67,114,62,159,68,64,103,163,65,156,27,104,110,116,118,17,117,161,154,14,33,25,40,21,30,150,35,124,42,12,146,19,122,9,38,29,151,8,6,148,126,130,3,4,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_72-OD2_54: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_72-OD2_54 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,96,95,97,101,80,79,108,91,74,60,89,46,112,67,114,62,159,68,64,103,163,65,156,27,104,110,116,118,17,117,161,154,14,33,25,40,21,30,150,35,124,42,12,146,19,122,9,38,29,151,8,6,148,126,130,3,4,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_87-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=93,48,35,42,112,38,114,50,110,89,91,60,33,40,59,27,65,74,64,76,77,122,95,97,96,67,124,30,68,29,116,117,118,80,79,130,25,146,132,159,163,126,156,161,136,127,154,140,150,138,12,142,9,14,6,148,19,21,17,151,3,2,4,8, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_108-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_108-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=93,48,35,42,112,38,114,50,110,89,91,60,33,40,59,27,65,74,64,76,77,122,95,97,96,67,124,30,68,29,116,117,118,80,79,130,25,146,132,159,163,126,156,161,136,127,154,140,150,138,12,142,9,14,6,148,19,21,17,151,3,2,4,8, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_101-O_56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_101-O_56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=93,48,35,42,112,38,114,50,110,89,91,60,33,40,59,27,65,74,64,76,77,122,95,97,96,67,124,30,68,29,116,117,118,80,79,130,25,146,132,159,163,126,156,161,136,127,154,140,150,138,12,142,9,14,6,148,19,21,17,151,3,2,4,8, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_72-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_72-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,95,96,97,101,80,79,108,74,91,60,46,89,67,112,114,62,159,68,64,163,103,65,156,27,104,110,116,118,17,117,161,154,14,25,33,40,21,30,150,35,42,124,12,146,19,122,9,38,29,151,8,6,148,3,126,4,130,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_HG1_93-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_93-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,95,96,97,101,80,79,108,74,91,60,46,89,67,112,114,62,159,68,64,163,103,65,156,27,104,110,116,118,17,117,161,154,14,25,33,40,21,30,150,35,42,124,12,146,19,122,9,38,29,151,8,6,148,3,126,4,130,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_87-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_87-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,95,96,97,101,80,79,108,74,91,60,46,89,67,112,114,62,159,68,64,163,103,65,156,27,104,110,116,118,17,117,161,154,14,25,33,40,21,30,150,35,42,124,12,146,19,122,9,38,29,151,8,6,148,3,126,4,130,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_46-OD1_53: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-OD1_53 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=76,77,48,59,95,96,97,101,80,79,108,74,91,60,46,89,67,112,114,62,159,68,64,163,103,65,156,27,104,110,116,118,17,117,161,154,14,25,33,40,21,30,150,35,42,124,12,146,19,122,9,38,29,151,8,6,148,3,126,4,130,2,127,136,132,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H2_3-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H2_3-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=151,146,150,9,6,8,127,124,154,161,136,126,27,12,25,19,29,122,138,46,156,163,117,116,130,118,30,14,21,112,50,110,40,33,132,51,142,159,48,17,140,108,114,42,60,35,93,103,59,101,62,38,104,87,91,68,72,65,67,96,95,97,89,64,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H3_4-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H3_4-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=151,146,150,9,6,8,127,124,154,161,136,126,27,12,25,19,29,122,138,46,156,163,117,116,130,118,30,14,21,112,50,110,40,33,132,51,142,159,48,17,140,108,114,42,60,35,93,103,59,101,62,38,104,87,91,68,72,65,67,96,95,97,89,64,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_2-O_165: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_2-O_165 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=151,146,150,9,6,8,127,124,154,161,136,126,27,12,25,19,29,122,138,46,156,163,117,116,130,118,30,14,21,112,50,110,40,33,132,51,142,159,48,17,140,108,114,42,60,35,93,103,59,101,62,38,104,87,91,68,72,65,67,96,95,97,89,64,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H2_3-OXT_166: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H2_3-OXT_166 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=151,146,150,9,127,6,8,124,161,154,136,126,27,12,25,19,122,29,138,163,156,117,116,46,118,130,30,112,14,50,21,110,40,33,159,132,51,142,48,140,108,17,114,42,60,35,93,103,59,101,62,104,38,91,87,72,68,65,96,97,95,67,89,64,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_146-O_23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_146-O_23 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6,29,46,9,25,126,151,122,161,154,8,30,12,40,33,130,19,138,50,112,116,117,110,118,51,48,108,163,156,132,14,142,21,42,35,140,114,60,159,103,101,93,17,59,62,38,104,87,72,91,65,68,67,96,97,95,64,89,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_101-O_70: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_101-O_70 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=101,72,65,103,87,104,67,76,38,77,89,80,79,68,59,35,42,60,108,93,51,48,91,95,97,46,96,33,40,50,114,112,110,30,27,29,122,124,132,25,130,140,116,118,117,159,142,17,163,146,136,126,156,14,138,21,127,161,12,19,154,150,6,9,8,148,3,4,2,151, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_HG1_114-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_HG1_114-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=89,159,46,110,116,118,117,48,72,163,103,156,104,77,76,122,59,62,27,161,74,154,124,79,60,80,146,150,40,33,42,35,67,64,148,38,65,126,151,25,68,30,130,29,127,9,12,14,19,17,136,21,132,6,8,3,4,2,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_108-OG1_92: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_108-OG1_92 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=89,159,46,110,116,118,117,48,72,163,103,156,104,77,76,122,59,62,27,161,74,154,124,79,60,80,146,150,40,33,42,35,67,64,148,38,65,126,151,25,68,30,130,29,127,9,12,14,19,17,136,21,132,6,8,3,4,2,138,140,142, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPD_H_46-O_120: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-O_120 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=122,110,25,150,29,40,33,161,30,154,116,117,118,114,101,93,163,103,60,127,156,9,126,148,136,42,35,59,6,151,62,12,130,87,159,19,3,4,2,72,104,8,14,91,38,21,132,138,65,68,17,67,96,95,97,89,140,64,142,76,77,74,80,79, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
# Speeding up H-bonds
cont_HB_hardF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=hbond_H_46-O_120,hbond_H_146-O_23,hbond_H_101-O_56,hbond_H_108-O_56,hbond_HG1_114-OG1_92,hbond_H_108-OG1_92, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
NWH_hardF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VA_H_46-O_120,VA_H_146-O_23,VA_H_101-O_56,VA_H_108-O_56,VA_HG1_114-OG1_92,VA_H_108-OG1_92, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WH SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NWO_hardF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=VH_H_46-O_120,VH_H_146-O_23,VH_H_101-O_56,VH_H_108-O_56,VH_HG1_114-OG1_92,VH_H_108-OG1_92, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
NPA_hardF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPA_H_46-O_120,NPA_H_146-O_23,NPA_H_101-O_56,NPA_H_108-O_56,NPA_HG1_114-OG1_92,NPA_H_108-OG1_92, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
NPD_hardF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPD_H_46-O_120,NPD_H_146-O_23,NPD_H_101-O_56,NPD_H_108-O_56,NPD_HG1_114-OG1_92,NPD_H_108-OG1_92, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cont_HB_softF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=87,87,93,93,72,72,3,4,2,3,101,87, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=54,53,54,53,54,53,165,165,165,166,70,56, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
NPA_softF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPA_H_87-OD2_54,NPA_H_87-OD1_53,NPA_HG1_93-OD2_54,NPA_HG1_93-OD1_53,NPA_H_72-OD2_54,NPA_H_72-OD1_53,NPA_H2_3-O_165,NPA_H3_4-O_165,NPA_H_2-O_165,NPA_H2_3-OXT_166,NPA_H_101-O_70,NPA_H_87-O_56, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
NPD_softF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPD_H_87-OD2_54,NPD_H_87-OD1_53,NPD_HG1_93-OD2_54,NPD_HG1_93-OD1_53,NPD_H_72-OD2_54,NPD_H_72-OD1_53,NPD_H2_3-O_165,NPD_H3_4-O_165,NPD_H_2-O_165,NPD_H2_3-OXT_166,NPD_H_101-O_70,NPD_H_87-O_56, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cont_HB_softU: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=46,46, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=53,54, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=8} PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
NPA_softU: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPA_H_46-OD1_53,NPA_H_46-OD2_54, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
NPD_softU: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=NPD_H_46-OD1_53,NPD_H_46-OD2_54, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Total
diffHB_compact: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cont_HB_hardF,NWH_hardF,NWO_hardF,NPA_hardF,NPD_hardF,cont_HB_softF,NPA_softF,NPD_softF,cont_HB_softU,NPA_softU,NPD_softU, COEFFICIENTS the coefficients of the arguments in your function=1.0,-0.0625,-0.125,-1.0,-0.5,1.0,-1.0,-0.5,-1.0,0.0,0.0, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Combine the H-bonds, non-compact
diff_H_46-O_120: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_H_46-O_120,NWH_H_46-O_120,NWO_H_46-O_120,NPA_H_46-O_120,NPD_H_46-O_120 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_146-O_23: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_H_146-O_23,NWH_H_146-O_23,NWO_H_146-O_23,NPA_H_146-O_23,NPD_H_146-O_23 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_101-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_H_101-O_56,NWH_H_101-O_56,NWO_H_101-O_56,NPA_H_101-O_56,NPD_H_101-O_56 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_108-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_H_108-O_56,NWH_H_108-O_56,NWO_H_108-O_56,NPA_H_108-O_56,NPD_H_108-O_56 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_HG1_114-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_HG1_114-OG1_92,NWH_HG1_114-OG1_92,NWO_HG1_114-OG1_92,NPA_HG1_114-OG1_92,NPD_HG1_114-OG1_92 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_108-OG1_92: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=hbond_H_108-OG1_92,NWH_H_108-OG1_92,NWO_H_108-OG1_92,NPA_H_108-OG1_92,NPD_H_108-OG1_92 VARthe names to give each of the arguments in the function=x,y,z,t,w FUNCthe function you wish to evaluate=x-y/16-z/8-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_87-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-OD2_54,NPA_H_87-OD2_54,NPD_H_87-OD2_54 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_87-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-OD1_53,NPA_H_87-OD1_53,NPD_H_87-OD1_53 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_HG1_93-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_HG1_93-OD2_54,NPA_HG1_93-OD2_54,NPD_HG1_93-OD2_54 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_HG1_93-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_HG1_93-OD1_53,NPA_HG1_93-OD1_53,NPD_HG1_93-OD1_53 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_72-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_72-OD2_54,NPA_H_72-OD2_54,NPD_H_72-OD2_54 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_72-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_72-OD1_53,NPA_H_72-OD1_53,NPD_H_72-OD1_53 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H2_3-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H2_3-O_165,NPA_H2_3-O_165,NPD_H2_3-O_165 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H3_4-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H3_4-O_165,NPA_H3_4-O_165,NPD_H3_4-O_165 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_2-O_165: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_2-O_165,NPA_H_2-O_165,NPD_H_2-O_165 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H2_3-OXT_166: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H2_3-OXT_166,NPA_H2_3-OXT_166,NPD_H2_3-OXT_166 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_101-O_70: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_101-O_70,NPA_H_101-O_70,NPD_H_101-O_70 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_87-O_56: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_87-O_56,NPA_H_87-O_56,NPD_H_87-O_56 VARthe names to give each of the arguments in the function=x,t,w FUNCthe function you wish to evaluate=x-t-w/2 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_46-OD1_53: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_46-OD1_53, VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diff_H_46-OD2_54: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=cont_H_46-OD2_54, VARthe names to give each of the arguments in the function=x FUNCthe function you wish to evaluate=-x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
diffHB_non_compact: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=diff_H_46-O_120,diff_H_146-O_23,diff_H_101-O_56,diff_H_108-O_56,diff_HG1_114-OG1_92,diff_H_108-OG1_92,diff_H_87-OD2_54,diff_H_87-OD1_53,diff_HG1_93-OD2_54,diff_HG1_93-OD1_53,diff_H_72-OD2_54,diff_H_72-OD1_53,diff_H2_3-O_165,diff_H3_4-O_165,diff_H_2-O_165,diff_H2_3-OXT_166,diff_H_101-O_70,diff_H_87-O_56,diff_H_46-OD1_53,diff_H_46-OD2_54  COEFFICIENTS the coefficients of the arguments in your function=1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Now for the side chains 
SC1: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=7,10,11,13,15,16,18,20 MASS calculate the center of mass
SC2: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=28,31,32,34,36,37,39,41 MASS calculate the center of mass
SC3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=49,52,53,54 MASS calculate the center of mass
SC4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=58,63,66 MASS calculate the center of mass
SC5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=75,78,81,82,83 MASS calculate the center of mass
SC6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=90,92,94 MASS calculate the center of mass
SC7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=102 MASS calculate the center of mass
SC8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=111,113,115 MASS calculate the center of mass
SC9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=125,128,129,131,133,134,135,137,139,141 MASS calculate the center of mass
SC10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=149,152,153,155,157,158,160,162,166 MASS calculate the center of mass
contside1-3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC3  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC4  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC5  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC6  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC7  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside1-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC4  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC5  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC6  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC7  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside2-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC5  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC6  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC7  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside3-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside4-6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC6  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside4-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC7  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside4-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside4-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside4-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside5-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC7  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside5-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside5-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside5-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside6-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC8  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside6-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside6-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside7-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC9  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside7-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
contside8-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC10  SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8}
SC1-3: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC3
SC1-4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC4
SC1-5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC5
SC1-6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC6
SC1-7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC7
SC1-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC8
SC1-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC9
SC1-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC1,SC10
SC2-4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC4
SC2-5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC5
SC2-6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC6
SC2-7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC7
SC2-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC8
SC2-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC9
SC2-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC2,SC10
SC3-5: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC5
SC3-6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC6
SC3-7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC7
SC3-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC8
SC3-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC9
SC3-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC3,SC10
SC4-6: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC4,SC6
SC4-7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC4,SC7
SC4-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC4,SC8
SC4-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC4,SC9
SC4-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC4,SC10
SC5-7: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC5,SC7
SC5-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC5,SC8
SC5-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC5,SC9
SC5-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC5,SC10
SC6-8: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC8
SC6-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC9
SC6-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC6,SC10
SC7-9: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC9
SC7-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC7,SC10
SC8-10: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=SC8,SC10
exc_SC2-4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2-4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC3,SC5,SC6,SC7,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC2-4: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside2-4,exc_SC2-4 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC2-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2-7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC3,SC4,SC5,SC6,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC2-7: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside2-7,exc_SC2-7 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC2-9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2-9 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC3,SC4,SC5,SC6,SC7,SC8,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC2-9: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside2-9,exc_SC2-9 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC3-5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3-5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC4,SC6,SC7,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC3-5: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside3-5,exc_SC3-5 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC3-6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3-6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC4,SC5,SC7,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC3-6: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside3-6,exc_SC3-6 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC3-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3-7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC4,SC5,SC6,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC3-7: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside3-7,exc_SC3-7 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC3-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3-8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC4,SC5,SC6,SC7,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC3-8: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside3-8,exc_SC3-8 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC3-10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC3-10 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC4,SC5,SC6,SC7,SC8,SC9, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC3-10: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside3-10,exc_SC3-10 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC4-7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC4-7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC3,SC5,SC6,SC8,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC4-7: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside4-7,exc_SC4-7 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
exc_SC6-8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC6-8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC1,SC2,SC3,SC4,SC5,SC7,SC9,SC10, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.35 NN=2 MM=10 D_MAX=0.5} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=0.8 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
diff_SC6-8: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contside6-8,exc_SC6-8 COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
contsideF: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=SC2,SC2,SC2,SC3,SC3,SC3,SC3,SC3,SC4,SC6, GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=SC4,SC7,SC9,SC5,SC6,SC7,SC8,SC10,SC7,SC8, SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.80 NN=4 MM=8} PAIR Pair only 1st element of the 1st group with 1st element in the second, etc
exSCF: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=exc_SC2-4,exc_SC2-7,exc_SC2-9,exc_SC3-5,exc_SC3-6,exc_SC3-7,exc_SC3-8,exc_SC3-10,exc_SC4-7,exc_SC6-8, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
cmap_compact: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=contsideF,exSCF COEFFICIENTS the coefficients of the arguments in your function=1.0,-1.0, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# Combine the side chain cmap
cmap_non_compact: COMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=diff_SC2-4,diff_SC2-7,diff_SC2-9,diff_SC3-5,diff_SC3-6,diff_SC3-7,diff_SC3-8,diff_SC3-10,diff_SC4-7,diff_SC6-8  COEFFICIENTS the coefficients of the arguments in your function=1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0, PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
C49: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=49 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
C55: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=55 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
C47: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=47 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
C52: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=52 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
N45: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=45 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
O56: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=56 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
O23: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=23 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.3 NN=6 MM=10 D_MAX=1.0} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opes
	ARGthe labels of the scalars on which the bias will act=diffHB_compact,cmap_compact
	SIGMA the initial widths of the kernels, divided by the square root of gamma=1.57,0.32
	FILE a file in which the list of all deposited kernels is stored=Kernels.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
	PACEthe frequency for kernel deposition=50000
	#RESTART=YES
	BARRIERthe free energy barrier to be overcome=20
... OPES_METAD_EXPLORE

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opese1
	ARGthe labels of the scalars on which the bias will act=C49
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.33
	FILE a file in which the list of all deposited kernels is stored=Kernelse1.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse1
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse1
	PACEthe frequency for kernel deposition=100000
	BARRIERthe free energy barrier to be overcome=3
	#RESTART=YES
... OPES_METAD_EXPLORE

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opese2
	ARGthe labels of the scalars on which the bias will act=C55
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.17
	FILE a file in which the list of all deposited kernels is stored=Kernelse2.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse2
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse2
	PACEthe frequency for kernel deposition=100000
	BARRIERthe free energy barrier to be overcome=3
	#RESTART=YES
... OPES_METAD_EXPLORE

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opese3
	ARGthe labels of the scalars on which the bias will act=C47
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.27
	FILE a file in which the list of all deposited kernels is stored=Kernelse3.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse3
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse3
	PACEthe frequency for kernel deposition=100000
	BARRIERthe free energy barrier to be overcome=3
	#RESTART=YES
... OPES_METAD_EXPLORE

OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
	LABELa label for the action so that its output can be referenced in the input to other actions=opese4
	ARGthe labels of the scalars on which the bias will act=C52
	SIGMA the initial widths of the kernels, divided by the square root of gamma=0.37
	FILE a file in which the list of all deposited kernels is stored=Kernelse4.data
	STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse4
	STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernelse4
	PACEthe frequency for kernel deposition=100000
	BARRIERthe free energy barrier to be overcome=3
	#RESTART=YES
... OPES_METAD_EXPLORE

ene: ENERGYCalculate the total potential energy of the simulation box. More details
ecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. More details ARGthe label of the internal energy of the system=ene TEMP_MINthe minimum of the temperature range=336 TEMP_MAXthe maximum of the temperature range=360
opesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=1000 UPDATE_FROMOnly update this action from this time=100

#1 339-342
#2 338-345
#3 337-350
#4 336-360
#5 335-380
#6 330-400
#7 320-420

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=opes.bias,ene,rmsd_ca,diffHB_compact,cmap_compact,C49,C55,C47,C52,N45,O56,O23,opesX.bias,opese1.bias,opese2.bias,opese3.bias,opese4.bias  FILEthe name of the file on which to output these quantities=COLVAR