Project ID: plumID:23.017
Source: classical_biased_MD/plumed.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=1-7654 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=npt_eqm3_align2z_CA.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL ################################################################################################## # --- (2) CONTACT DESCRIPTORS ---
#....Reactive Criteria 1............ Dnu1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 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=0.55 NN=6 MM=10} Dnu2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 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=0.55 NN=6 MM=10}
Nu1-CH2OH: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7716 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} Nu2-CH2OH: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7716 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}
Nu1-acid: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 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} Nu2-acid: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 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}
#....Reactive Criteria 2............ Dacid: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7698 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=0.45 NN=6 MM=10}
#....Reactive Criteria 3............ strHbond-O21: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4654 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7703 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} strHbond-O22: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4655 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7703 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}
strHbond-O31: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4654 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7707 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} strHbond-O32: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4655 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7707 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}
D300_torsion: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4646,4648,4650,4653 #N-CA-CB-CG torsion of residue 300 cos_torsion: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=D300_torsion FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=-1,1 # --- Z-distance DESCRIPTOR --- D197CA: 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=3020 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=7678-7719 #The reactive rings of the ligand (residue 500 and 501) D_nu-lig: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=D197CA,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label
################################################################################################## # --- (3) WATER DESCRIPTORS ---
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=7765-67992:3 #water molecules
ligO4: 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=7698 #Solvation of ligand (resid 500) ligO2: 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=7703 #Solvation of ligand (resid 501) ligO3: 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=7707 #Solvation of ligand (resid 501) ligO6: 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=7716 #Solvation of ligand (resid 501)
D197: 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=3025 #Bindong pose selected atom D300: 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=4653 #Bindong pose selected atom
# Hydration spots v1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.4475,4.6727,5.4427 v2: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.5887,4.7353,5.3047 v3: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.7473,4.5323,5.2327 v4: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.7796,4.6265,5.1469 v5: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.9981,4.6302,5.2047 v6: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=5.1255,4.7229,5.2486 v7: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=5.0725,4.8750,5.2862 v8: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=4.8496,4.9004,5.2126 v9: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=5.0243,5.0961,5.3479 v10: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=5.0874,5.2668,5.3580 # --- DESCRIPTORS --- NligO2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=ligO2 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 NligO3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=ligO3 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 NligO4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=ligO4 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 NligO6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=ligO6 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 ND197: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=D197 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 ND300: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=D300 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 # ---(4) Wall on distance to prevent exit of ligand LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0.65 ARGthe arguments on which the bias is acting=D_nu-lig.z KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=lower_wall_z UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1.00 ARGthe arguments on which the bias is acting=D_nu-lig.z KAPPAthe force constant for the wall=10000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_wall_z
################################################################################################## # --- (5) Two deepTDA CVs ---
s_contact: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=contactCV_model.ptc ARGthe labels of the values from which the function is calculated=Dnu1,Dnu2,Nu1-CH2OH,Nu2-CH2OH,Nu1-acid,Nu2-acid,strHbond-O21,strHbond-O22,strHbond-O31,strHbond-O32,Dacid,cos_torsion,D_nu-lig.z UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=15.0 ARGthe arguments on which the bias is acting=s_contact.node-0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_wall_s_contact LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=-15.0 ARGthe arguments on which the bias is acting=s_contact.node-0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=lower_wall_s_contact
#............................................................................................ s_water: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=water_model.ptc ARGthe labels of the values from which the function is calculated=cvwo1,cvwo2,cvwo3,cvwo4,cvwo5,cvwo6,cvwo7,cvwo8,cvwo9,cvwo10,NligO2,NligO3,NligO4,NligO6,ND197,ND300 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=15.0 ARGthe arguments on which the bias is acting=s_water.node-0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_wall_s_water LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=-15.0 ARGthe arguments on which the bias is acting=s_water.node-0 KAPPAthe force constant for the wall=5000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=lower_wall_s_water
#.....normalized deepCV................................................................ n_s_contact: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s_contact.node-0 FUNCthe function you wish to evaluate=(x+14.0)/28.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO n_s_water: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=s_water.node-0 FUNCthe function you wish to evaluate=(x+14.0)/28.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #.....pathCV................................................................ pth: PATHPath collective variables with a more flexible framework for the distance metric being used. This action is a shortcut. More details REFERENCEa pdb file containing the set of reference configurations=final_path.pdb TYPE the manner in which distances are calculated=EUCLIDEAN LAMBDAthe lambda parameter is needed for smoothing, is in the units of plumed=200.0 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0.01 ARGthe arguments on which the bias is acting=pth.zpath KAPPAthe force constant for the wall=500000 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_pthz
################################################################################################## # --- (6) OPES ---
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. 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=pth.spath 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=500 BARRIERthe free energy barrier to be overcome=55 TEMP temperature=300.0 # RESTART=YES STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=5000 WALKERS_MPI switch on MPI version of multiple walkers ... OPES_METAD
PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=100 ARGthe labels of the values that you would like to print to the file=s_contact.node-0,s_water.node-0,n_s_contact,n_s_water,pth.spath,pth.zpath,*.bias,opes.rct,opes.zed,opes.neff,opes.nker FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f