Project ID: plumID:22.002
Source: OAH-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
Click on the labels of the actions for more information on what each action computes
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# 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_static_few.cpp #GAMBES_log.cpp #LOAD FILE=GAMBES_test1.cpp #LIGAND/HOST CAL: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=29-212the 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 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 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=222-6521:3the 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. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.0 v2:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.25 v3:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.5 v4:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.75 v5:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.0 v6:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.25 v7:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,3.5 v8:coordinates of the virtual atomFIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=cvwo8the input to this functionFUNC=(x/2.8)-1.0the function you wish to evaluatePERIODIC=NO ################################if the output of your function is periodic then you should specify the periodicity of the function
#NEW ANGLE angcalg:ANGLECalculate 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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_OAH_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_OAH_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_OAH_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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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:ENERGYCalculate the total potential energy of the simulation box. More details
cbhak:COORDINATIONCalculate 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=3 ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z PACE=500 FILENAME=nstate BIAS_CUTOFF CUTOFF=110 # STATIC_BIAS_OPTIMIZE # STATIC_FACTORS=1,0.28,-1 STATIC_BIAS STATIC_FACTORS=1,0.28,0.5 ... GAMBESLThis action is not part of PLUMED and was included by using a LOAD command More details
# #PRINT ARG=autoA.node-0,autoB.node-0,cvwo2,cyl.z,cvwo3,autoC.node-0,funnelwall.bias,upper_wall.bias,cvwo1,sang,cang,radius,Acube,Bcube,Ccube,cbhak,cswo1,cswo2,cswo3,cswo4,cvwo7,ene STRIDE=250 FILE=COLVARmeta FMT=%8.4fPrint 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=%8.4fthe 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,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=%8.9f #PRINT ARG=radius,cyl.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