**Project ID:** plumID:22.002

**Source:** OAMe-G4/plumed.dat

**Originally used with PLUMED version:** 2.6

**Stable:** zipped raw stdout - zipped raw stderr - stderr

**Master:** zipped raw stdout - zipped raw stderr - stderr

# vim:ft=plumed#RESTARTEnables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=GAMBES_log.cpp #LIGAND/HOSTfile to be loadedLC: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 detailsATOMS=29-34,36-37,39-44,46-49,52-53,55-59,62-71,73-75,77-79,81-83,85-108,116-121,123-135,137,139,144,151-160the numerical indexes for the set of atoms in the groupLOW: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 detailsATOMS=29-68the numerical indexes for the set of atoms in the groupCAL: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 detailsATOMS=29-224the numerical indexes for the set of atoms in the groupL1:ATOMS=63,65,41,31 #lower exagonthe numerical indexes for the set of atoms in the groupL2:ATOMS=58,42,56,33 #lower exagonthe numerical indexes for the set of atoms in the groupHCAL:ATOMS=29-160the numerical indexes for the set of atoms in the group

#GUESTGC:ATOMS=1-11 #,10-12the numerical indexes for the set of atoms in the groupGO:ATOMS=12-13the numerical indexes for the set of atoms in the groupGBr:ATOMS=14the numerical indexes for the set of atoms in the groupGSEL:ATOMS=2,3,11,14the numerical indexes for the set of atoms in the groupl1:ATOMS=2the numerical indexes for the set of atoms in the groupl2:ATOMS=3the numerical indexes for the set of atoms in the groupl3:ATOMS=11the numerical indexes for the set of atoms in the groupl4:ATOMS=14the numerical indexes for the set of atoms in the group

#WaterNa:ATOMS=225-233the numerical indexes for the set of atoms in the group

#WaterWO:ATOMS=234-6533:3the numerical indexes for the set of atoms in the groupWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=the atoms that make up a molecule that you wish to alignCALFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsSTRIDE=1the frequency with which molecules are reassembledREFERENCE=conf_template.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedlig:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor forGC#checkpock:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=29-68 ##DISTANCE ATOMS=pock,lig LABEL=d1 COMPONENTSthe group of atoms that you are calculating the Gyration Tensor forv1:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.0coordinates of the virtual atomv2:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.25coordinates of the virtual atomv3:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.5coordinates of the virtual atomv4:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.75coordinates of the virtual atomv5:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.0coordinates of the virtual atomv6:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.25coordinates of the virtual atomv7:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.5coordinates of the virtual atomv8:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.75coordinates of the virtual atomVIRT:ATOMS=the numerical indexes for the set of atoms in the groupv1,v2,v3,v4,v5,v6,v7,v8cyl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenv1,ligCOMPONENTS#NEW DISTANCEcalculate the x, y and z components of the distance separately and store them as labelcswo1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsl1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WOSWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcswo2:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsl2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WOSWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcswo3:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsl3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WOSWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH}This keyword is used if you want to employ an alternative to the continuous switching function defined aboveNLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcswo4:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsl4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo2:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv2GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo3:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv3GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo4:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv4GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo5:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv5GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo6:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv6GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo7:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv7GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listcvwo8:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv8GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.4The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor listd1:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=the input to this functioncswo1FUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functiond2:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=the input to this functioncswo2FUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functiond3:MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=the input to this functioncswo3FUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the functiond4:ARG=the input to this functioncswo4FUNC=(x/2.5)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond5:ARG=the input to this functioncvwo1FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond6:ARG=the input to this functioncvwo2FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond7:ARG=the input to this functioncvwo3FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond8:ARG=the input to this functioncvwo4FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond9:ARG=the input to this functioncvwo5FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond10:ARG=the input to this functioncvwo6FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond11:ARG=the input to this functioncvwo7FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functiond12:ARG=the input to this functioncvwo8FUNC=(x/2.8)-1.0the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the function

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#NEW ANGLElowcal:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor forL1highcal:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=the group of atoms that you are calculating the Gyration Tensor forL2angcalg:ANGLECalculate an angle. More detailsATOMS=the list of atoms involved in this collective variable (either 3 or 4 atoms)v3,v5,6,11sang:ARG=the input to this functionangcalgFUNC=sin(xthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functioncang:ARG=the input to this functionangcalgFUNC=cos(xthe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the function

#Funnelradius:ARG=the input to this functioncyl.x,cyl.yVAR=x,ythe names to give each of the arguments in the functionFUNC=sqrt(x*x+y*ythe function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionfunnel:ARG=the input to this functionradius,cyl.zVAR=r,zthe names to give each of the arguments in the functionFUNC=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=0the positions of the wallARG=the arguments on which the bias is actingfunnelKAPPA=2000.0the force constant for the wallLABEL=a label for the action so that its output can be referenced in the input to other actionsfunnelwall

# Wall on distance to prevent the protein breakingUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsAT=1.8the positions of the wallARG=the arguments on which the bias is actingcyl.zKAPPA=4000.0the force constant for the wallEXP=2the powers for the wallsLABEL=a label for the action so that its output can be referenced in the input to other actionsupper_wallautoA:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1a.ptFilename of the PyTorch compiled modelARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12autoB:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1b.ptFilename of the PyTorch compiled modelARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12autoC:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1c.ptFilename of the PyTorch compiled modelARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12Acube:ARG=the input to this functionautoA.node-0FUNC=x+x^3the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionBcube:ARG=the input to this functionautoB.node-0FUNC=x+x^3the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionCcube:ARG=the input to this functionautoC.node-0FUNC=x+x^3the function you wish to evaluateif the output of your function is periodic then you should specify the periodicity of the functionene:ENERGYCalculate the total potential energy of the simulation box. More detailscbhak:COORDINATIONCalculate coordination numbers. More detailsGROUPA=First list of atomsv1GROUPB=Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)WONLISTUse a neighbor list to speed up the calculationNL_CUTOFF=1.0The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor list

################################GAMBESL... LABEL=This action is not part of PLUMED and was included by using a LOAD command More detailsgambesNSTATES=1 ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.zFILENAME=dstate PACE=500 BIAS_CUTOFF CUTOFF=30 ... GAMBESLCOMMITTOR...Does a committor analysis. More detailsARG=the input for this action is the scalar output from one or more other actionscyl.z,AcubeSTRIDE=250the frequency with which the CVs are analyzedBASIN_LL1=0.9,-2List of lower limits for basin #BASIN_UL1=1.2,3 ... COMMITTORList of upper limits for basin #Print quantities to a file. More detailsARGthe input for this action is the scalar output from one or more other actionsSTRIDE=250the frequency with which the quantities of interest should be outputFILE=COLVARthe name of the file on which to output these quantitiesFMT=%8.4f #PRINT ARG=autoA.node-0,autoB.node-0,swo1,d1.z,swo2,autoC.node-0,funnelwall.bias,upper_wall.bias,opes.bias,opes.rct,swo3,opes.nker,sang,cang,radius,Acube,Bcube,Ccube,swo4,opes.*,ene STRIDE=250 FILE=COLVARmeta FMT=%8.4fthe format that should be used to output real numbersPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionsd1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,radius,cbhak,ene,gambes.biasSTRIDE=250the frequency with which the quantities of interest should be outputFILE=COLVARNNthe name of the file on which to output these quantitiesFMT=%8.4f #PRINT ARG=swo1,swo2,swo3,swo4,vwo1,vwo2,vwo3,vwo4,vwo5,vwo6,vwo7,vwo8,radius,d1.z,ene STRIDE=250 FILE=COLVARNN FMT=%8.4f #PRINT ARG=radius,d1.z STRIDE=250 FILE=COLVARbuca FMT=%8.4fthe format that should be used to output real numbersPrint quantities to a file. More detailsARG=the input for this action is the scalar output from one or more other actionscyl.z,Acube,gambesSTRIDE=250the frequency with which the quantities of interest should be outputFILE=col_descthe name of the file on which to output these quantitiesFMT=%8.9fthe format that should be used to output real numbersFLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More detailsSTRIDE=10the frequency with which all the open files should be flushedENDPLUMEDTerminate plumed input. More details