Project ID: plumID:24.029
Source: Trypsin_Benzamidine/explore/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=1-3232 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
# 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
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 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: MATHEVAL ARG=NG FUNC=(x/1.5)-1.0 PERIODIC=NO #FH: MATHEVAL ARG=NH FUNC=(x/2.5)-1.0 PERIODIC=NO
# ---(3) Funnel --- 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 radius: 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=cyl.x,cyl.y VARthe names to give each of the arguments in the function=x,y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO funnel: 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=radius,cyl.z VARthe names to give each of the arguments in the function=r,z FUNCthe function you wish to evaluate=(r+0.5*(-1.6+z))*step(-z+1.2)+(r-0.2)*step(z-1.2) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0 ARGthe arguments on which the bias is acting=funnel KAPPAthe force constant for the wall=10000.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnelwall
# ---(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=0.2 ARGthe arguments on which the bias is acting=cyl.z 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_z UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=3.0 ARGthe arguments on which the bias is acting=cyl.z 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_z
# ---(5) This rmsd restricts the CA momevement of the entire protein rmsdINIT: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details 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 UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsdINIT ATthe positions of the wall=0.09 KAPPAthe force constant for the wall=420000 EXP the powers for the walls=2 OFFSET the offset for the start of the wall=0 LABELa label for the action so that its output can be referenced in the input to other actions=rmsdwallINIT
# --- (6) DEEP-LDA CV --- #s: PYTORCH_MODEL FILE=CV_16V_G_H_1.pt ARG=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH #sw: MATHEVAL ARG=s.node-0 FUNC=x+x^3 PERIODIC=NO
#UPPER_WALLS AT=3.0 ARG=sw KAPPA=4000.0 EXP=2 LABEL=upper_sw #LOWER_WALLS AT=-3.0 ARG=sw KAPPA=5000.0 EXP=2 LABEL=lower_sw
# --- (7) DEEP-TICA CV ---
#t: PYTORCH_MODEL FILE=deeptica_all_lag_0.07model_all.pt ARG=vwo14,vwo3,vwo5,vwo9,vwo7,vwo10,vwo12,vwo11,vwo6,vwo2,vwo16,vwo1,vwo15,vwo8,vwo13,vwo4,FG,FH #st: MATHEVAL ARG=t.node-0 FUNC=1*x PERIODIC=NO
# --- (8) EXCLUDED region ____
#target: CUSTOM ARG=cyl.z FUNC=step(x-0.6) PERIODIC=NO
OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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=opesE ARGthe labels of the scalars on which the bias will act=cyl.z FILE a file in which the list of all deposited kernels is stored=KernelsE.data STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressedE.Kernels PACEthe frequency for kernel deposition=500 BARRIERthe free energy barrier to be overcome=40 #EXCLUDED_REGION=target RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO #STATE_WSTRIDE=5000 ... OPES_METAD_EXPLORE
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,opesE.bias STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=COLVAR_all FMTthe format that should be used to output real numbers=%8.4f