PLUMED-NEST

Project ID: plumID:24.024
Source: OneOpes_input_files/CB8/CB8_S6-G0/4/plumed.dat
Originally used with PLUMED version: 2.9
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

# --- (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=47-190      #host atoms
The GROUP action with label HOST calculates somethingLIGC: 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=1-24  #carbon atoms in the ligand
The GROUP action with label LIGC calculates somethingl1: 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=9             #ligand selected atoms
The GROUP action with label l1 calculates somethingl2: 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=13
The GROUP action with label l2 calculates somethingl3: 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
The GROUP action with label l3 calculates somethingl4: 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
The GROUP action with label l4 calculates somethingWO: 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=191-4324:3    #water oxygen atoms

The GROUP action with label WO calculates somethingWHOLEMOLECULESThis 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
The WHOLEMOLECULES action with label  calculates somethingFIT_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

The CENTER action with label lig calculates the following quantities:
 Quantity   
 Description  
lig.value
the position of the center of massv1: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,0.0   #virtual atoms
The FIXEDATOM action with label v1 calculates somethingv2: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,0.25
The FIXEDATOM action with label v2 calculates somethingv3: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,0.5
The FIXEDATOM action with label v3 calculates somethingv4: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,0.75
The FIXEDATOM action with label v4 calculates somethingv5: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,1
The FIXEDATOM action with label v5 calculates somethingv6: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,1.25
The FIXEDATOM action with label v6 calculates somethingv7: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,-0.25
The FIXEDATOM action with label v7 calculates somethingv8: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,-0.5
The FIXEDATOM action with label v8 calculates somethingv9: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,-0.75
The FIXEDATOM action with label v9 calculates somethingv10: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,-1.0
The FIXEDATOM action with label v10 calculates somethingv11: FIXEDATOMAdd a virtual atom in a fixed position. More details ATcoordinates of the virtual atom=0.0,0.0,-1.25

The FIXEDATOM action with label v11 calculates somethingcyl: 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
The DISTANCE action with label cyl calculates the following quantities:
 Quantity   
 Description  
cyl.x
the x-component of the vector connecting the two atoms
cyl.y
the y-component of the vector connecting the two atoms
cyl.z
the z-component of the vector connecting the two atoms
cyl.value
the DISTANCE between this pair of atomsradius: 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 ---

The MATHEVAL action with label radius calculates the following quantities:
 Quantity   
 Description  
radius.value
an arbitrary functionL1: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label L1 calculates the following quantities:
 Quantity   
 Description  
L1.value
the value of the coordinationL2: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label L2 calculates the following quantities:
 Quantity   
 Description  
L2.value
the value of the coordinationL3: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label L3 calculates the following quantities:
 Quantity   
 Description  
L3.value
the value of the coordinationL4: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label L4 calculates the following quantities:
 Quantity   
 Description  
L4.value
the value of the coordinationV1: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V1 calculates the following quantities:
 Quantity   
 Description  
V1.value
the value of the coordinationV2: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V2 calculates the following quantities:
 Quantity   
 Description  
V2.value
the value of the coordinationV3: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V3 calculates the following quantities:
 Quantity   
 Description  
V3.value
the value of the coordinationV4: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V4 calculates the following quantities:
 Quantity   
 Description  
V4.value
the value of the coordinationV5: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V5 calculates the following quantities:
 Quantity   
 Description  
V5.value
the value of the coordinationV6: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V6 calculates the following quantities:
 Quantity   
 Description  
V6.value
the value of the coordinationV7: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V7 calculates the following quantities:
 Quantity   
 Description  
V7.value
the value of the coordinationV8: 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V8 calculates the following quantities:
 Quantity   
 Description  
V8.value
the value of the coordinationV9: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v9 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V9 calculates the following quantities:
 Quantity   
 Description  
V9.value
the value of the coordinationV10: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v10 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label V10 calculates the following quantities:
 Quantity   
 Description  
V10.value
the value of the coordinationV11: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=v11 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 D_MAX=0.8} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=1.5 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20


The COORDINATION action with label V11 calculates the following quantities:
 Quantity   
 Description  
V11.value
the value of the coordinationlig_torsion1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=4,10,15,18
The TORSION action with label lig_torsion1 calculates the following quantities:
 Quantity   
 Description  
lig_torsion1.value
the TORSION involving these atomslig_torsion2: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=15,18,19,20
The TORSION action with label lig_torsion2 calculates the following quantities:
 Quantity   
 Description  
lig_torsion2.value
the TORSION involving these atomslig_torsion3: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=11,15,18,19

# --- (3) Funnel, walls and angle definitions ---

The TORSION action with label lig_torsion3 calculates the following quantities:
 Quantity   
 Description  
lig_torsion3.value
the TORSION involving these atomsfunnel: 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+0.8*(-0.75+z))*step(-z+0.5)+(r-0.2)*step(z-0.5))*step(z-0.0)+((r-0.8*(0.75+z))*step(z+0.5)+(r-0.2)*step(-z-0.5))*step(-z+0.0) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label funnel calculates the following quantities:
 Quantity   
 Description  
funnel.value
an arbitrary functionUPPER_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
The UPPER_WALLS action with label funnelwall calculates the following quantities:
 Quantity   
 Description  
funnelwall.bias
the instantaneous value of the bias potential
funnelwall.force2
the instantaneous value of the squared force due to this bias potentialUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=1.5 ARGthe arguments on which the bias is acting=cyl.z 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=upper_wall
The UPPER_WALLS action with label upper_wall calculates the following quantities:
 Quantity   
 Description  
upper_wall.bias
the instantaneous value of the bias potential
upper_wall.force2
the instantaneous value of the squared force due to this bias potentialLOWER_WALLSDefines a wall for the value of one or more collective variables, More details ATthe positions of the wall=-1.5 ARGthe arguments on which the bias is acting=cyl.z 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=lower_wall


The LOWER_WALLS action with label lower_wall calculates the following quantities:
 Quantity   
 Description  
lower_wall.bias
the instantaneous value of the bias potential
lower_wall.force2
the instantaneous value of the squared force due to this bias potentialang: ANGLECalculate one or multiple angle/s. More details ATOMSthe list of atoms involved in this collective variable (either 3 or 4 atoms)=v3,v5,9,20   #angle of a ligand's axis with z
The ANGLE action with label ang calculates the following quantities:
 Quantity   
 Description  
ang.value
the ANGLE involving these atomscosang: 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
The MATHEVAL action with label cosang calculates the following quantities:
 Quantity   
 Description  
cosang.value
an arbitrary functionene: ENERGYCalculate the total potential energy of the simulation box. More details
# --- (4) OPES  ---

The ENERGY action with label ene calculates somethingecv: ECV_MULTITHERMALExpand a simulation to sample multiple temperatures simultaneously. More details ARGthe label of the internal energy of the system=ene TEMP_MAXthe maximum of the temperature range=310
The ECV_MULTITHERMAL action with label ecv calculates the following quantities:
 Quantity   
 Description  
ecv..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsopesX: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=ecv.* FILE a file with the estimate of the relative Delta F for each component of the target and of the global c(t)=DeltaFs.data PACEhow often the bias is updated=100


The OPES_EXPANDED action with label opesX calculates the following quantities:
 Quantity   
 Description  
opesX.bias
the instantaneous value of the bias potentialOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. 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,cosang
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.047,0.082
   FILE a file in which the list of all deposited kernels is stored=Kernels.data
   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
   PACEthe frequency for kernel deposition=10000
   BARRIERthe free energy barrier to be overcome=100
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opese1
   ARGthe labels of the scalars on which the bias will act=L4,lig_torsion1,lig_torsion2
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.29,0.26,2.1
   FILE a file in which the list of all deposited kernels is stored=Kernels1.data
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels1.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels1.data
   PACEthe frequency for kernel deposition=20000
   BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opese1 calculates the following quantities:
 Quantity   
 Description  
opese1.bias
the instantaneous value of the bias potential
opese1.rct
estimate of c(t)
opese1.zed
estimate of Z_n
opese1.neff
effective sample size
opese1.nker
total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opese2
   ARGthe labels of the scalars on which the bias will act=V1,lig_torsion2,lig_torsion3
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.29,2.1,3
   FILE a file in which the list of all deposited kernels is stored=Kernels2.data
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels2.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels2.data
   PACEthe frequency for kernel deposition=20000
   BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opese2 calculates the following quantities:
 Quantity   
 Description  
opese2.bias
the instantaneous value of the bias potential
opese2.rct
estimate of c(t)
opese2.zed
estimate of Z_n
opese2.neff
effective sample size
opese2.nker
total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opese3
   ARGthe labels of the scalars on which the bias will act=L1,lig_torsion3,lig_torsion1
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.17,3,0.26
   FILE a file in which the list of all deposited kernels is stored=Kernels3.data
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels3.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels3.data
   PACEthe frequency for kernel deposition=20000
   BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opese3 calculates the following quantities:
 Quantity   
 Description  
opese3.bias
the instantaneous value of the bias potential
opese3.rct
estimate of c(t)
opese3.zed
estimate of Z_n
opese3.neff
effective sample size
opese3.nker
total number of compressed kernels used to represent the biasOPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details ...
   LABELa label for the action so that its output can be referenced in the input to other actions=opese4
   ARGthe labels of the scalars on which the bias will act=V3,lig_torsion1,lig_torsion2
SIGMA the initial widths of the kernels, divided by the square root of gamma=0.29,0.26,2.1
   FILE a file in which the list of all deposited kernels is stored=Kernels4.data
   STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed_Kernels4.data
   STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels4.data
   PACEthe frequency for kernel deposition=20000
   BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE

The OPES_METAD_EXPLORE action with label opese4 calculates the following quantities:
 Quantity   
 Description  
opese4.bias
the instantaneous value of the bias potential
opese4.rct
estimate of c(t)
opese4.zed
estimate of Z_n
opese4.neff
effective sample size
opese4.nker
total number of compressed kernels used to represent the biasPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=opes.bias,cyl.z,radius,funnelwall.bias,upper_wall.bias,lower_wall.bias,ene,cosang,L1,L2,L3,L4,V1,V2,V3,V4,V5,V6,V7,V8,V9,V10,V11,opesX.bias,opese1.bias,opese2.bias,opese3.bias,opese4.bias,lig_torsion1,lig_torsion2,lig_torsion3 STRIDE the frequency with which the quantities of interest should be output=500 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