Project ID: plumID:23.009
Source: OAMe_G2/training/flooding/template/plumed_data.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
# vim: ft=plumed# # --- (0) LOAD PYTORCH ---Enables syntax highlighting for PLUMED files in vim. See here for more details.
#LOAD FILE=../code/PytorchModel.cpp
# --- (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=16-211 #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=221-6520:3 #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 ---
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}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=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}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=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}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=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}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=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}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=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}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=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}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=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}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=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}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=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}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=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}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=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}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
d1:MATHEVALAn alias to the ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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 ef CUSTOM function. 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_MODEL MODEL=modelG2_a.pt ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 #NN output #sw: MATHEVAL ARG=s.node-0 FUNC=x+x^3 PERIODIC=NO #Deep-LDA CV
#funnel: MATHEVAL ARG=radius,cyl.z VAR=r,z FUNC=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODIC=NO #UPPER_WALLS AT=0 ARG=funnel KAPPA=2000.0 LABEL=funnelwall #funnel restraint #UPPER_WALLS AT=1.8 ARG=cyl.z KAPPA=4000.0 EXP=2 LABEL=upper_wall #upper limit of cyl.z
#ang: ANGLE ATOMS=v3,v5,8,6 #angle of a ligand's axis with z #cosang: MATHEVAL ARG=ang FUNC=cos(x) PERIODIC=NO
# --- (4) OPES Flooding --- #target: CUSTOM ARG=cyl.z FUNC=step(x-1.0) PERIODIC=NO
#OPES_METAD ... # LABEL=opes # ARG=cyl.z # FILE=Kernels.data # RESTART=NO # STATE_RFILE=compressed_Kernels.data # STATE_WFILE=compressed_Kernels.data # PACE=500 # BARRIER=40 # EXCLUDED_REGION=target # #SIGMA=0.05 #... OPES_METAD
#COMMITTOR ... # ARG=cyl.z # STRIDE=50000 # BASIN_LL1=1.6 # BASIN_UL1=2.0 #... COMMITTORPrint quantities to a file. More detailsARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.zthe 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=data.datthe name of the file on which to output these quantitiesENDPLUMEDTerminate plumed input. More details