Project ID: plumID:22.002
Source: OAH-G2/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# --- (0) LOAD PYTORCH and OPES ---Enables syntax highlighting for PLUMED files in vim. See here for more details.
#LOAD FILE=../code/PytorchModel.cppLOADLoads a library, possibly defining new actions. More detailsFILE=GAMBES_log.cppfile to be loaded
# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---
HOST: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=16-199 #host atoms LIGC: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=1-7,9 #carbon atoms in the ligand 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=1 #ligand selected atoms 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=4 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=8 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=9 WO: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=209-6508:3 #water oxygen atomsthe 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=HOSTthe 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 #coordinates alignment lig:the manner in which RMSD alignment is performedCENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=LIGCthe 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 #virtual atoms 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=2.0136,2.0136,3.75coordinates of the virtual atom
cyl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=v1,ligthe pair of atom that we are calculating the distance betweenCOMPONENTSradius:calculate the x, y and z components of the distance separately and store them as labelMATHEVALAn alias to the ef CUSTOM function. More detailsARG=cyl.x,cyl.ythe input to this functionFUNC=sqrt(x*x+y*ythe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# --- (2) DESCRIPTORS --- 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=5 #L: COORDINATION GROUPA=l1,l2,l3,l4 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST NL_CUTOFF=1.4 NL_STRIDE=5 #V: COORDINATION GROUPA=v1,v2,v3,v4,v5,v6,v7,v8 GROUPB=WO SWITCH={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST NL_CUTOFF=1.4 NL_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 #normalized descriptors 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
# --- (3) DEEP-LDA CV and other quantities ---
sa:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG2_OAH_a.ptFilename of the PyTorch compiled modelARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 #NN output sw:the input for this action is the scalar output from one or more other actionsMATHEVALAn alias to the ef CUSTOM function. More detailsARG=sa.node-0the input to this functionFUNC=x+x^3the function you wish to evaluatePERIODIC=NO #Deep-LDA CVif the output of your function is periodic then you should specify the periodicity of the function
funnel:MATHEVALAn 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=funnelwall #funnel restrainta label for the action so that its output can be referenced in the input to other actionsUPPER_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_wall #upper limit of cyl.za label for the action so that its output can be referenced in the input to other actions
ang:ANGLECalculate an angle. More detailsATOMS=v3,v5,8,6 #angle of a ligand's axis with z cosang:the list of atoms involved in this collective variable (either 3 or 4 atoms)MATHEVALAn alias to the ef CUSTOM function. More detailsARG=angthe 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
ene:ENERGYCalculate the total potential energy of the simulation box. More details
# --- (4) GAMBES ---GAMBESL... LABEL=gambes ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z NSTATES=1 FILENAME=nstate PACE=500 BIAS_CUTOFF CUTOFF=70 ... 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,swthe input for this action is the scalar output from one or more other actionsSTRIDE=10the frequency with which the CVs are analyzedBASIN_LL1=1.16,2.1 #BASIN_LL1=1.06,2.08List of lower limits for basin #BASIN_UL1=2,3 ... COMMITTORList of upper limits for basin #Print quantities to a file. More detailsARG=cyl.z,sw,gambesthe input for this action is the scalar output from one or more other actionsSTRIDE=1the 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 numbersPrint quantities to a file. More detailsARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,sw,gambesthe input for this action is the scalar output from one or more other actionsSTRIDE=125the frequency with which the quantities of interest should be outputFILE=COLVARNNthe name of the file on which to output these quantitiesFMT=%8.9fthe format that should be used to output real numbersPrint 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 numbersENDPLUMEDTerminate plumed input. More details