Project ID: plumID:22.002
Source: OAMe-G4/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
tested onv2.10
tested onmaster
tested on master
# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 
#RESTART
LOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=GAMBES_log.cpp
#LIGAND/HOST
LC: 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=29-34,36-37,39-44,46-49,52-53,55-59,62-71,73-75,77-79,81-83,85-108,116-121,123-135,137,139,144,151-160
LOW: 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=29-68
CAL: 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=29-224
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=63,65,41,31   #lower exagon
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=58,42,56,33   #lower exagon
HCAL: 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=29-160

#GUEST
GC: 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=1-11 #,10-12
GO: 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=12-13
GBr: 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=14
GSEL: 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=2,3,11,14
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=2
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=11
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=14

#Water
Na: 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=225-233

#Water
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=234-6533:3

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=CAL
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
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=GC  #check
pock: 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=29-68
##DISTANCE ATOMS=pock,lig LABEL=d1  COMPONENTS 

v1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.0 v2: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.25 v3: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.5 v4: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,2.75 v5: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.0 v6: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.25 v7: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.5 v8: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=2.0136,2.0136,3.75 VIRT: 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=v1,v2,v3,v4,v5,v6,v7,v8 cyl: DISTANCECalculate the distance between a pair 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 #NEW DISTANCE
cswo1: 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={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cswo2: 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={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cswo3: 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={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cswo4: 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={RATIONAL D_0=0.0 R_0=0.25 NN=6 MM=10 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo1: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo2: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo3: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo4: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo5: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo6: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo7: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=5 cvwo8: 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={RATIONAL D_0=0.0 R_0=0.25 NN=2 MM=6 D_MAX=1.0 NOSTRETCH} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.4 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=cswo1 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 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=cswo2 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=cswo3 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=cswo4 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=cvwo1 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=cvwo2 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=cvwo3 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=cvwo4 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=cvwo5 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=cvwo6 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=cvwo7 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=cvwo8 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 ################################
#NEW ANGLE lowcal: 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=L1 highcal: 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=L2 angcalg: ANGLECalculate an angle. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=v3,v5,6,11 sang: 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=angcalg FUNCthe function you wish to evaluate=sin(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO cang: 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=angcalg 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 #Funnel 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 VARthe names to give each of the arguments in the function=x,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 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
# Wall on distance to prevent the protein breaking 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
autoA: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1a.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 autoB: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1b.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 autoC: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=modelG4_NN_UW_OW1c.pt ARGthe labels of the values from which the function is calculated=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12 Acube: 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=autoA.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 Bcube: 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=autoB.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 Ccube: 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=autoC.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 ene: ENERGYCalculate the total potential energy of the simulation box. More details cbhak: 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={RATIONAL D_0=0.0 R_0=0.35 NN=16 MM=32} 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 ################################ GAMBESLThis action is not part of PLUMED and was included by using a LOAD command More details ... LABEL=gambes NSTATES=1 ARG=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z FILENAME=dstate PACE=500 BIAS_CUTOFF CUTOFF=30 ... GAMBESL COMMITTORDoes a committor analysis. More details ... ARGthe labels of the values which is being used to define the committor surface=cyl.z,Acube STRIDE the frequency with which the CVs are analyzed=250 BASIN_LL1List of lower limits for basin #=0.9,-2 BASIN_UL1List of upper limits for basin #=1.2,3 ... COMMITTOR 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 #PRINT ARG=autoA.node-0,autoB.node-0,swo1,d1.z,swo2,autoC.node-0,funnelwall.bias,upper_wall.bias,opes.bias,opes.rct,swo3,opes.nker,sang,cang,radius,Acube,Bcube,Ccube,swo4,opes.*,ene STRIDE=250 FILE=COLVARmeta FMT=%8.4f PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,cyl.z,radius,cbhak,ene,gambes.bias STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=COLVARNN FMTthe format that should be used to output real numbers=%8.4f #PRINT ARG=swo1,swo2,swo3,swo4,vwo1,vwo2,vwo3,vwo4,vwo5,vwo6,vwo7,vwo8,radius,d1.z,ene STRIDE=250 FILE=COLVARNN FMT=%8.4f #PRINT ARG=radius,d1.z STRIDE=250 FILE=COLVARbuca FMT=%8.4f PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cyl.z,Acube,gambes.* STRIDE the frequency with which the quantities of interest should be output=250 FILEthe name of the file on which to output these quantities=col_desc FMTthe format that should be used to output real numbers=%8.9f FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=10 ENDPLUMEDTerminate plumed input. More details