Project ID: plumID:20.025
Source: OAH_G1/plumed.dat
Originally used with PLUMED version: 2.5
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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# --- (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 details ATOMSthe numerical indexes for the set of atoms in the group=16-199 #host atoms LIGC: 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 details ATOMSthe numerical indexes for the set of atoms in the group=1-6 #carbon atoms in the ligand l1: 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 details ATOMSthe numerical indexes for the set of atoms in the group=1 #ligand selected atoms l2: 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 details ATOMSthe numerical indexes for the set of atoms in the group=3 l3: 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 details ATOMSthe numerical indexes for the set of atoms in the group=4 l4: 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 details ATOMSthe numerical indexes for the set of atoms in the group=6 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 details ATOMSthe numerical indexes for the set of atoms in the group=209-6508:3 #water oxygen atoms
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=HOST FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=conf_template.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL #coordinates alignment lig: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=LIGC v1: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0 #virtual atoms v2: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.25 v3: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5 v4: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.75 v5: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0 v6: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.25 v7: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.5 v8: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.75
cyl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=v1,lig COMPONENTS calculate the x, y and z components of the distance separately and store them as label radius: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=cyl.x,cyl.y FUNCthe function you wish to evaluate=sqrt(x*x+y*y) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- (2) DESCRIPTORS ---
L1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 L2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 L3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 L4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=l4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v2 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V3: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v3 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V4: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V5: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v5 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V6: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v6 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V7: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v7 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 V8: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v8 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=WO SWITCHThis keyword is used if you want to employ an alternative to the continuous switching function defined above. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 d1: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L1 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #normalized descriptors d2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L2 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d3: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L3 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d4: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=L4 FUNCthe function you wish to evaluate=(x/2.5)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d5: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V1 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d6: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V2 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d7: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V3 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d8: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V4 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d9: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V5 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d10: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V6 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d11: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V7 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO d12: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=V8 FUNCthe function you wish to evaluate=(x/2.8)-1.0 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO # --- (3) DEEP-LDA CV and other quantities ---
s: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG1_OAH_a.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 #NN output sw: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=s.node-0 FUNCthe function you wish to evaluate=x+x^3 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO #Deep-LDA CV
funnel: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=radius,cyl.z VARthe names to give each of the arguments in the function=r,z FUNCthe function you wish to evaluate=(r+1.0*(-1.2+z))*step(-z+1.)+(r-0.2)*step(z-1.) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=0 ARGthe arguments on which the bias is acting=funnel KAPPAthe force constant for the wall=2000.0 LABELa label for the action so that its output can be referenced in the input to other actions=funnelwall #funnel restraint UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1.8 ARGthe arguments on which the bias is acting=cyl.z KAPPAthe force constant for the wall=4000.0 EXP the powers for the walls=2 LABELa label for the action so that its output can be referenced in the input to other actions=upper_wall #upper limit of cyl.z
ang: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=v3,v5,8,6 #angle of a ligand's axis with z cosang: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=ang FUNCthe function you wish to evaluate=cos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO ene: ENERGYCalculate the total potential energy of the simulation box. More details
# --- (4) OPES ---
OPES_METADOn-the-fly probability enhanced sampling with metadynamics-like target distribution. This action has hidden defaults. More details ... LABELa label for the action so that its output can be referenced in the input to other actions=opes ARGthe labels of the scalars on which the bias will act=cyl.z,sw BARRIERthe free energy barrier to be overcome=50 PACEthe frequency for kernel deposition=500 FILE a file in which the list of all deposited kernels is stored=../Kernels.data RESTARTallows per-action setting of restart (YES/NO/AUTO)=NO STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=../compressed_Kernels.data STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=../compressed_Kernels.data STATE_WSTRIDEnumber of MD steps between writing the STATE_WFILE=50000 WALKERS_MPI switch on MPI version of multiple walkers ... OPES_METAD
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVAR FMTthe format that should be used to output real numbers=%8.4f ENDPLUMEDTerminate plumed input. More details