**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

# 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 loadedHOST: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 atomsthe numerical indexes for the set of atoms in the groupLIGC: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=1-6,8-10 #carbon atoms in the ligandthe numerical indexes for the set of atoms in the groupl1: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 #ligand selected atomsthe numerical indexes for the set of atoms in the groupl2:ATOMS=4the numerical indexes for the set of atoms in the groupl3:ATOMS=6the numerical indexes for the set of atoms in the groupl4:ATOMS=7the numerical indexes for the set of atoms in the groupWO:ATOMS=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=the atoms that make up a molecule that you wish to alignHOSTFIT_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 alignmentthe 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 forLIGCv1:FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More detailsAT=2.0136,2.0136,2.0 #virtual atomscoordinates 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 atomcyl:DISTANCECalculate the distance between a pair of atoms. More detailsATOMS=the pair of atom that we are calculating the distance betweenv1,ligCOMPONENTScalculate the x, y and z components of the distance separately and store them as labelradius: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 functioncyl.x,cyl.yFUNC=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=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 listL2: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 listL3: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 listL4: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 listV1: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 listV2: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 listV3: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 listV4: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 listV5: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 listV6: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 listV7: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 listV8: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 functionL1FUNC=(x/2.5)-1.0the function you wish to evaluatePERIODIC=NO #normalized descriptorsif 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 functionL2FUNC=(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:ARG=the input to this functionL3FUNC=(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 functiond4:ARG=the input to this functionL4FUNC=(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 functionV1FUNC=(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 functionV2FUNC=(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 functionV3FUNC=(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 functionV4FUNC=(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 functionV5FUNC=(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 functionV6FUNC=(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 functionV7FUNC=(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 functionV8FUNC=(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

# --- (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=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#NN outputsw:ARG=the input to this functions.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 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#funnel restraintUPPER_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_wall#upper limit of s_zang:ANGLECalculate an angle. More detailsATOMS=the list of atoms involved in this collective variable (either 3 or 4 atoms)v3,v5,8,6 #angle of a ligand's axis with zcosang:ARG=the input to this functionangFUNC=cos(xthe 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 detailsGAMBESL... ARG=This action is not part of PLUMED and was included by using a LOAD command More detailsd1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.zNSTATES=2 FILENAME=nstate LABEL=gambesPACE=500 BIAS_CUTOFF CUTOFF=70 STATIC_BIAS STATIC_FACTORS=1,0.1138 ... GAMBESLCOMMITTOR...Does a committor analysis. More detailsARG=the input for this action is the scalar output from one or more other actionscyl.z,swSTRIDE=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=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,gambes.biasSTRIDE=250the frequency with which the quantities of interest should be outputFILE=COLVARNNthe name of the file on which to output these quantitiesFMT=%8.4fthe 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,sw,gambesSTRIDE=250the frequency with which the quantities of interest should be outputFILE=col_descthe name of the file on which to output these quantitiesFMT=%8.4fthe format that should be used to output real numbersENDPLUMEDTerminate plumed input. More details