Project ID: plumID:24.029
Source: Trypsin_Benzamidine/analysis_scripts/plumed_driver.dat
Originally used with PLUMED version: 2.9
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
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# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---
protein: 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=1-3232 WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=protein FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=fit_tem.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL 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=3251-47362:3 # water molecules
G: 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=3236 #ligand selected atom H: 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=2480 #Bindong pose selected atom
lig: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=3233,3236,3237,3240,3241,3243,3245,3247,3249 #Carbon and Nitrogen atoms of the ligand
# Hydration spots v1: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.710,3.472,4.707 v2: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.600,3.300,4.400 v3: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.731,3.025,3.992 v4: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.705,3.084,3.683 v5: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.883,3.174,3.461 v6: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.040,3.264,3.306 v7: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.239,3.319,3.236 v8: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.485,3.286,3.225 v9: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.701,3.182,3.332 v10: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.466,3.382,3.446 v11: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.461,3.424,3.659 v12: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.495,3.335,3.920 v13: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.295,3.430,3.876 v14: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=4.070,3.450,3.834 v15: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.887,3.241,3.875 v16: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=3.815,3.292,4.144
# --- (2) DESCRIPTORS --- NG: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G 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=0.25 NN=6 MM=10 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 NH: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=H 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=6 MM=10 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v1 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v2 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v3 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v4 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v5 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v6 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v7 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v8 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v9 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v10 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v11 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo12: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v12 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo13: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v13 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo14: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v14 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo15: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v15 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 cvwo16: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v16 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=0.25 NN=2 MM=6 D_MAX=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20 vwo1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo1 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #normalized descriptors vwo2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo2 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo3: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo3 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo4: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo4 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo5: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo5 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo6: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo6 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo7: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo7 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo8: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo8 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo9: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo9 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo10: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo10 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo11: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo11 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo12: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo12 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo13: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo13 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo14: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo14 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo15: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo15 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO vwo16: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cvwo16 FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FG: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=NG FUNCthe function you wish to evaluate=(x/1.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO FH: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=NH FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO cyl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=v14,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=water_cv_features.dat FMTthe format that should be used to output real numbers=%8.4f