Project ID: plumID:22.002
Source: OAH-G3/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# --- (1) ATOMS DEFINITIONS and ALIGNMENT ---Enables syntax highlighting for PLUMED files in vim. See here for more details.LOADLoads a library, possibly defining new actions. More detailsFILE=GAMBES_log.cppfile to be loaded
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=33-216 #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=1-6,8-10 #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=6 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=7 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=224-6523:3 #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. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.0 #virtual atoms 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=2.0136,2.0136,3.75coordinates 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 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 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 ---
L1: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 L2: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 L3: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 L4: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 V1: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 V2: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 V3: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 V4: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 V5: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 V6: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 V7: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 V8: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=L1the 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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=L2the 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=L3the 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=L4the 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=V1the 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=V2the 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=V3the 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=V4the 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=V5the 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=V6the 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=V7the 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=V8the 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 ---
s:PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More detailsFILE=modelG3_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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More detailsARG=s.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 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=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 s_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 CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. 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 detailsGAMBESL... ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z NSTATES=2 FILENAME=nstate LABEL=gambes PACE=500 BIAS_CUTOFF CUTOFF=70 STATIC_BIAS STATIC_FACTORS=1,0.1138 ... 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=1.1,2List of lower limits for basin #BASIN_UL1=2,3 ... COMMITTORList of upper limits for basin #
# --- (4) OPES ---Print quantities to a file. More detailsARGthe 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=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,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=%8.4fthe format that should be used to output real numbersPrint quantities to a file. More detailsARG=cyl.z,sw,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=%8.4fthe format that should be used to output real numbersENDPLUMEDTerminate plumed input. More details