Project ID: plumID:22.028
Source: plumed_M9.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
######### PLUMED file for performing RECT simulations on N-glycans ######### #MOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=reference_M9.pdb # # Define torsion angles for M9 # phi1_2:a file in pdb format containing a reference structureTORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-2,the O5 atom in residue 2. Click here for more information.@C1-2,the C1 atom in residue 2. Click here for more information.@O4-1,the O4 atom in residue 1. Click here for more information.@C4-1psi1_2:the C4 atom in residue 1. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-2,the C1 atom in residue 2. Click here for more information.@O4-1,the O4 atom in residue 1. Click here for more information.@C4-1,the C4 atom in residue 1. Click here for more information.@C3-1# phi2_3:the C3 atom in residue 1. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-3,the O5 atom in residue 3. Click here for more information.@C1-3,the C1 atom in residue 3. Click here for more information.@O4-2,the O4 atom in residue 2. Click here for more information.@C4-2psi2_3:the C4 atom in residue 2. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-3,the C1 atom in residue 3. Click here for more information.@O4-2,the O4 atom in residue 2. Click here for more information.@C4-2,the C4 atom in residue 2. Click here for more information.@C3-2# phi3_4:the C3 atom in residue 2. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-4,the O5 atom in residue 4. Click here for more information.@C1-4,the C1 atom in residue 4. Click here for more information.@O3-3,the O3 atom in residue 3. Click here for more information.@C3-3psi3_4:the C3 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-4,the C1 atom in residue 4. Click here for more information.@O3-3,the O3 atom in residue 3. Click here for more information.@C3-3,the C3 atom in residue 3. Click here for more information.@C2-3# phi4_5:the C2 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-5,the O5 atom in residue 5. Click here for more information.@C1-5,the C1 atom in residue 5. Click here for more information.@O2-4,the O2 atom in residue 4. Click here for more information.@C2-4psi4_5:the C2 atom in residue 4. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-5,the C1 atom in residue 5. Click here for more information.@O2-4,the O2 atom in residue 4. Click here for more information.@C2-4,the C2 atom in residue 4. Click here for more information.@C1-4# phi5_6:the C1 atom in residue 4. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-6,the O5 atom in residue 6. Click here for more information.@C1-6,the C1 atom in residue 6. Click here for more information.@O2-5,the O2 atom in residue 5. Click here for more information.@C2-5psi5_6:the C2 atom in residue 5. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-6,the C1 atom in residue 6. Click here for more information.@O2-5,the O2 atom in residue 5. Click here for more information.@C2-5,the C2 atom in residue 5. Click here for more information.@C1-5the C1 atom in residue 5. Click here for more information.
phi3_7:TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-7,the O5 atom in residue 7. Click here for more information.@C1-7,the C1 atom in residue 7. Click here for more information.@O6-3,the O6 atom in residue 3. Click here for more information.@C6-3psi3_7:the C6 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-7,the C1 atom in residue 7. Click here for more information.@O6-3,the O6 atom in residue 3. Click here for more information.@C6-3,the C6 atom in residue 3. Click here for more information.@C5-3omega3_7:the C5 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O6-3,the O6 atom in residue 3. Click here for more information.@C6-3,the C6 atom in residue 3. Click here for more information.@C5-3,the C5 atom in residue 3. Click here for more information.@O5-3# phi7_8:the O5 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-8,the O5 atom in residue 8. Click here for more information.@C1-8,the C1 atom in residue 8. Click here for more information.@O3-7,the O3 atom in residue 7. Click here for more information.@C3-7psi7_8:the C3 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-8,the C1 atom in residue 8. Click here for more information.@O3-7,the O3 atom in residue 7. Click here for more information.@C3-7,the C3 atom in residue 7. Click here for more information.@C2-7# phi8_9:the C2 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-9,the O5 atom in residue 9. Click here for more information.@C1-9,the C1 atom in residue 9. Click here for more information.@O2-8,the O2 atom in residue 8. Click here for more information.@C2-8psi8_9:the C2 atom in residue 8. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-9,the C1 atom in residue 9. Click here for more information.@O2-8,the O2 atom in residue 8. Click here for more information.@C2-8,the C2 atom in residue 8. Click here for more information.@C1-8# phi7_10:the C1 atom in residue 8. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-10,the O5 atom in residue 10. Click here for more information.@C1-10,the C1 atom in residue 10. Click here for more information.@O6-7,the O6 atom in residue 7. Click here for more information.@C6-7psi7_10:the C6 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-10,the C1 atom in residue 10. Click here for more information.@O6-7,the O6 atom in residue 7. Click here for more information.@C6-7,the C6 atom in residue 7. Click here for more information.@C5-7omega7_10:the C5 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O6-7,the O6 atom in residue 7. Click here for more information.@C6-7,the C6 atom in residue 7. Click here for more information.@C5-7,the C5 atom in residue 7. Click here for more information.@O5-7# phi10_11:the O5 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@O5-11,the O5 atom in residue 11. Click here for more information.@C1-11,the C1 atom in residue 11. Click here for more information.@O2-10,the O2 atom in residue 10. Click here for more information.@C2-10psi10_11:the C2 atom in residue 10. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@C1-11,the C1 atom in residue 11. Click here for more information.@O2-10,the O2 atom in residue 10. Click here for more information.@C2-10,the C2 atom in residue 10. Click here for more information.@C1-10# # Define puckering for each monosaccharide only to print it to file # puck1:the C1 atom in residue 10. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-1,the O5 atom in residue 1. Click here for more information.@C1-1,the C1 atom in residue 1. Click here for more information.@C2-1,the C2 atom in residue 1. Click here for more information.@C3-1,the C3 atom in residue 1. Click here for more information.@C4-1,the C4 atom in residue 1. Click here for more information.@C5-1puck2:the C5 atom in residue 1. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-2,the O5 atom in residue 2. Click here for more information.@C1-2,the C1 atom in residue 2. Click here for more information.@C2-2,the C2 atom in residue 2. Click here for more information.@C3-2,the C3 atom in residue 2. Click here for more information.@C4-2,the C4 atom in residue 2. Click here for more information.@C5-2puck3:the C5 atom in residue 2. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-3,the O5 atom in residue 3. Click here for more information.@C1-3,the C1 atom in residue 3. Click here for more information.@C2-3,the C2 atom in residue 3. Click here for more information.@C3-3,the C3 atom in residue 3. Click here for more information.@C4-3,the C4 atom in residue 3. Click here for more information.@C5-3puck4:the C5 atom in residue 3. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-4,the O5 atom in residue 4. Click here for more information.@C1-4,the C1 atom in residue 4. Click here for more information.@C2-4,the C2 atom in residue 4. Click here for more information.@C3-4,the C3 atom in residue 4. Click here for more information.@C4-4,the C4 atom in residue 4. Click here for more information.@C5-4puck5:the C5 atom in residue 4. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-5,the O5 atom in residue 5. Click here for more information.@C1-5,the C1 atom in residue 5. Click here for more information.@C2-5,the C2 atom in residue 5. Click here for more information.@C3-5,the C3 atom in residue 5. Click here for more information.@C4-5,the C4 atom in residue 5. Click here for more information.@C5-5puck6:the C5 atom in residue 5. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-6,the O5 atom in residue 6. Click here for more information.@C1-6,the C1 atom in residue 6. Click here for more information.@C2-6,the C2 atom in residue 6. Click here for more information.@C3-6,the C3 atom in residue 6. Click here for more information.@C4-6,the C4 atom in residue 6. Click here for more information.@C5-6puck7:the C5 atom in residue 6. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-7,the O5 atom in residue 7. Click here for more information.@C1-7,the C1 atom in residue 7. Click here for more information.@C2-7,the C2 atom in residue 7. Click here for more information.@C3-7,the C3 atom in residue 7. Click here for more information.@C4-7,the C4 atom in residue 7. Click here for more information.@C5-7puck8:the C5 atom in residue 7. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-8,the O5 atom in residue 8. Click here for more information.@C1-8,the C1 atom in residue 8. Click here for more information.@C2-8,the C2 atom in residue 8. Click here for more information.@C3-8,the C3 atom in residue 8. Click here for more information.@C4-8,the C4 atom in residue 8. Click here for more information.@C5-8puck9:the C5 atom in residue 8. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-9,the O5 atom in residue 9. Click here for more information.@C1-9,the C1 atom in residue 9. Click here for more information.@C2-9,the C2 atom in residue 9. Click here for more information.@C3-9,the C3 atom in residue 9. Click here for more information.@C4-9,the C4 atom in residue 9. Click here for more information.@C5-9puck10:the C5 atom in residue 9. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-10,the O5 atom in residue 10. Click here for more information.@C1-10,the C1 atom in residue 10. Click here for more information.@C2-10,the C2 atom in residue 10. Click here for more information.@C3-10,the C3 atom in residue 10. Click here for more information.@C4-10,the C4 atom in residue 10. Click here for more information.@C5-10puck11:the C5 atom in residue 10. Click here for more information.PUCKERINGCalculate sugar pseudorotation coordinates. More detailsATOMS=the five or six atoms of the sugar ring in the proper order@O5-11,the O5 atom in residue 11. Click here for more information.@C1-11,the C1 atom in residue 11. Click here for more information.@C2-11,the C2 atom in residue 11. Click here for more information.@C3-11,the C3 atom in residue 11. Click here for more information.@C4-11,the C4 atom in residue 11. Click here for more information.@C5-11# # Define torsion angles required for J-coupling calculations # J3_7:the C5 atom in residue 11. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@H5-3,the H5 atom in residue 3. Click here for more information.@C5-3,the C5 atom in residue 3. Click here for more information.@C6-3,the C6 atom in residue 3. Click here for more information.@H61-3J3_7P:the H61 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@H5-3,the H5 atom in residue 3. Click here for more information.@C5-3,the C5 atom in residue 3. Click here for more information.@C6-3,the C6 atom in residue 3. Click here for more information.@H62-3# J7_10:the H62 atom in residue 3. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@H5-7,the H5 atom in residue 7. Click here for more information.@C5-7,the C5 atom in residue 7. Click here for more information.@C6-7,the C6 atom in residue 7. Click here for more information.@H61-7J7_10P:the H61 atom in residue 7. Click here for more information.TORSIONCalculate a torsional angle. More detailsATOMS=the four atoms involved in the torsional angle@H5-7,the H5 atom in residue 7. Click here for more information.@C5-7,the C5 atom in residue 7. Click here for more information.@C6-7,the C6 atom in residue 7. Click here for more information.@H62-7# # Apply 1D metadynamics on each torsion angle. Different bias potentials are applied in different replicas, according to the RECT keyword. # metaD_phi1_2:the H62 atom in residue 7. Click here for more information.METADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi1_2the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi1_2 metaD_psi1_2:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi1_2the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi1_2 # metaD_phi2_3:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi2_3the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi2_3 metaD_psi2_3:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi2_3the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi2_3 # metaD_phi3_4:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi3_4the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi3_4 metaD_psi3_4:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi3_4the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi3_4 # metaD_phi4_5:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi4_5the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi4_5 metaD_psi4_5:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi4_5the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi4_5 # metaD_phi5_6:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi5_6the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi5_6 metaD_psi5_6:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi5_6the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi5_6 # metaD_phi3_7:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi3_7the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi3_7 metaD_psi3_7:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi3_7the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi3_7 metaD_omega3_7:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=omega3_7the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_omega3_7 # metaD_phi7_8:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi7_8the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi7_8 metaD_psi7_8:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi7_8the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi7_8 # metaD_phi8_9:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi8_9the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi8_9 metaD_psi8_9:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi8_9the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi8_9 # metaD_phi7_10:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi7_10the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi7_10 metaD_psi7_10:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi7_10the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi7_10 metaD_omega7_10:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=omega7_10the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_omega7_10 # metaD_phi10_11:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=phi10_11the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_phi10_11 metaD_psi10_11:a file in which the list of added hills is storedMETADUsed to performed metadynamics on one or more collective variables. More detailsARG=psi10_11the input for this action is the scalar output from one or more other actionsTAU=4.0in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tauPACE=500the frequency for hill additionSIGMA=0.35the widths of the Gaussian hillsGRID_MIN=-pithe lower bounds for the gridGRID_MAX=pithe upper bounds for the gridGRID_BIN=200the number of bins for the gridTEMP=310.15the system temperature - this is only needed if you are doing well-tempered metadynamicsRECT=1,1.2,1.46,1.82,2.3,2.94,3.78,4.89,6.34,8.23,10.7,14list of bias factors for all the replicasFILE=HILLS_psi10_11 # # PRINT torsion angle values and puckering coordinates to separate files #a file in which the list of added hills is storedPrint quantities to a file. More detailsARG=phi1_2,psi1_2,phi2_3,psi2_3,phi3_4,psi3_4,phi4_5,psi4_5,phi5_6,psi5_6,phi3_7,psi3_7,omega3_7,phi7_8,psi7_8,phi8_9,psi8_9,phi7_10,psi7_10,omega7_10,phi10_11,psi10_11the input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=COLVAR #the name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=puck1.theta,puck2.theta,puck3.theta,puck4.theta,puck5.theta,puck6.theta,puck7.theta,puck8.theta,puck9.theta,puck10.theta,puck11.theta,puck1.phi,puck2.phi,puck3.phi,puck4.phi,puck5.phi,puck6.phi,puck7.phi,puck8.phi,puck9.phi,puck10.phi,puck11.phithe input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=COLVAR_theta #the name of the file on which to output these quantitiesPrint quantities to a file. More detailsARG=omega3_7,J3_7,J3_7P,omega7_10,J7_10,J7_10Pthe input for this action is the scalar output from one or more other actionsSTRIDE=200the frequency with which the quantities of interest should be outputFILE=COLVAR_NMR #the name of the file on which to output these quantities