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/HOST LC:file to be loadedGROUPDefine 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=29-34,36-37,39-44,46-49,52-53,55-59,62-71,73-75,77-79,81-83,85-108,116-121,123-135,137,139,144,151-160 LOW:the numerical indexes for the set of atoms in the groupGROUPDefine 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=29-68 CAL:the numerical indexes for the set of atoms in the groupGROUPDefine 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=29-224 L1:the numerical indexes for the set of atoms in the groupGROUPDefine 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=63,65,41,31 #lower exagon L2:the numerical indexes for the set of atoms in the groupGROUPDefine 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=58,42,56,33 #lower exagon HCAL:the numerical indexes for the set of atoms in the groupGROUPDefine 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=29-160the numerical indexes for the set of atoms in the group
#GUEST GC: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=1-11 #,10-12 GO:the numerical indexes for the set of atoms in the groupGROUPDefine 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=12-13 GBr:the numerical indexes for the set of atoms in the groupGROUPDefine 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=14 GSEL:the numerical indexes for the set of atoms in the groupGROUPDefine 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=2,3,11,14 l1:the numerical indexes for the set of atoms in the groupGROUPDefine 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=2 l2:the numerical indexes for the set of atoms in the groupGROUPDefine 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=3 l3:the numerical indexes for the set of atoms in the groupGROUPDefine 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=11 l4:the numerical indexes for the set of atoms in the groupGROUPDefine 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=14the numerical indexes for the set of atoms in the group
#Water Na: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=225-233the numerical indexes for the set of atoms in the group
#Water 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 detailsATOMS=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=CALthe atoms that make up a molecule that you wish to alignFIT_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=OPTIMAL lig:the manner in which RMSD alignment is performedCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=GC #check pock:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate 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 for
v1:FIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,2.0 v2:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,2.25 v3:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,2.5 v4:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,2.75 v5:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,3.0 v6:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,3.25 v7:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,3.5 v8:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. More detailsAT=2.0136,2.0136,3.75 VIRT:coordinates of the virtual atomGROUPDefine 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=v1,v2,v3,v4,v5,v6,v7,v8the numerical indexes for the set of atoms in the group
cyl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=v1,ligthe pair of atom that we are calculating the distance betweenCOMPONENTS#NEW DISTANCEcalculate the x, y and z components of the distance separately and store them as label
cswo1:COORDINATIONCalculate coordination numbers. More detailsGROUPA=l1First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={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=5 cswo2:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=l2First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={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=5 cswo3:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=l3First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={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=5 cswo4:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=l4First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={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=5 cvwo1:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v1First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo2:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v2First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo3:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v3First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo4:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v4First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo5:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v5First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo6:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v6First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo7:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v7First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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=5 cvwo8:The frequency with which we are updating the atoms in the neighbor listCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v8First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 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 list
d1:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=cswo1the input to this functionFUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NO d2:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cswo2the input to this functionFUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NO d3:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cswo3the input to this functionFUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NO d4:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cswo4the input to this functionFUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NO d5:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo1the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d6:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo2the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d7:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo3the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d8:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo4the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d9:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo5the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d10:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo6the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d11:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo7the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO d12:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cvwo8the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
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#NEW ANGLE lowcal:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=L1 highcal:the group of atoms that you are calculating the Gyration Tensor forCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=L2 angcalg:the group of atoms that you are calculating the Gyration Tensor forANGLECalculate an angle. More detailsATOMS=v3,v5,6,11 sang:the list of atoms involved in this collective variable (either 3 or 4 atoms)MATHEVALAn alias to the ef CUSTOM function. More detailsARG=angcalgthe input to this functionFUNC=sin(xthe function you wish to evaluatePERIODIC=NO cang:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=angcalgthe input to this functionFUNC=cos(xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
#Funnel radius:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=cyl.x,cyl.ythe input to this functionVAR=x,ythe names to give each of the arguments in the functionFUNC=sqrt(x*x+y*ythe function you wish to evaluatePERIODIC=NO funnel:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=radius,cyl.zthe input to this functionVAR=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 evaluatePERIODIC=NOif 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=funnelthe arguments on which the bias is actingKAPPA=2000.0the force constant for the wallLABEL=funnelwalla label for the action so that its output can be referenced in the input to other actions
# 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=cyl.zthe arguments on which the bias is actingKAPPA=4000.0the force constant for the wallEXP=2the powers for the wallsLABEL=upper_walla label for the action so that its output can be referenced in the input to other actions
autoA:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1a.ptFilename of the PyTorch compiled modelARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 autoB:the input for this action is the scalar output from one or more other actionsPYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1b.ptFilename of the PyTorch compiled modelARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 autoC:the input for this action is the scalar output from one or more other actionsPYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG4_NN_UW_OW1c.ptFilename of the PyTorch compiled modelARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12the input for this action is the scalar output from one or more other actions
Acube:MATHEVALAn alias to the ef CUSTOM function. More detailsARG=autoA.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NO Bcube:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=autoB.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NO Ccube:if the output of your function is periodic then you should specify the periodicity of the functionMATHEVALAn alias to the ef CUSTOM function. More detailsARG=autoC.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
ene:ENERGYcbhak:Calculate the total potential energy of the simulation box. More detailsCOORDINATIONCalculate coordination numbers. More detailsGROUPA=v1First list of atomsGROUPB=WOSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)SWITCH={RATIONAL D_0=0.0 R_0=0.35 NN=16 MM=32}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=1.0The cutoff for the neighbor listNL_STRIDE=5The frequency with which we are updating the atoms in the neighbor list
################################GAMBESL... LABEL=gambes NSTATES=1 ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z FILENAME=dstate PACE=500 BIAS_CUTOFF CUTOFF=30 ... GAMBESLThis action is not part of PLUMED and was included by using a LOAD command More detailsCOMMITTOR...Does a committor analysis. More detailsARG=cyl.z,Acubethe input for this action is the scalar output from one or more other actionsSTRIDE=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=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,radius,cbhak,ene,gambes.biasthe 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=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=cyl.z,Acube,gambesthe 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=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