PLUMED-NEST

Project ID: plumID:24.017
Source: BRD4/MetaDynamics/lig1/run6/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

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#  plumed.dat for Funnel MetaD in the WTE + PT #
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#RESTART

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### DEFINE RADIUS + CALC PROT-LIG VECTOR COMP ###
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MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../whole.pdb
The MOLINFO action with label  calculates somethingprotein: 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=1-2121
The GROUP action with label protein calculates somethingligand: 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=2122-2199
The GROUP action with label ligand calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details STRIDE the frequency with which molecules are reassembled=1 ENTITY0the atoms that make up a molecule that you wish to align=protein ENTITY1the atoms that make up a molecule that you wish to align=ligand
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=ligand AROUNDreference atoms=1586 GROUPBY group atoms so as not to break molecules=78 #random CA close to the binding pocket for pmas_d in chain B
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### DEFINITION_OF_COMs ###
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lig: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=ligand
The COM action with label lig calculates somethingp0: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1105,1461,1473,1521
The COM action with label p0 calculates somethingp1: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=824,846,1122,1586,1739,1774

The COM action with label p1 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=2200-33777:3


# Ligand atoms to solvate
The GROUP action with label WO calculates somethingG1: 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=2138
The GROUP action with label G1 calculates somethingG2: 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=2134
The GROUP action with label G2 calculates somethingG3: 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=2124

The GROUP action with label G3 calculates somethingNG1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G1 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NG1 calculates the following quantities:
 Quantity   
 Description  
NG1.value
the value of the coordinationNG2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G2 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NG2 calculates the following quantities:
 Quantity   
 Description  
NG2.value
the value of the coordinationNG3:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=G3  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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

# Protein atoms to solvate
The COORDINATION action with label NG3 calculates the following quantities:
 Quantity   
 Description  
NG3.value
the value of the coordinationP1: 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=1590 # CYS 95
The GROUP action with label P1 calculates somethingP2: 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=1647 # TYR 98
The GROUP action with label P2 calculates somethingP3: 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=934 # TYR 56
The GROUP action with label P3 calculates somethingP4: 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=1528 # MET 91


The GROUP action with label P4 calculates somethingNP1: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P1 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NP1 calculates the following quantities:
 Quantity   
 Description  
NP1.value
the value of the coordinationNP2: COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P2 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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NP2 calculates the following quantities:
 Quantity   
 Description  
NP2.value
the value of the coordinationNP3:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P3  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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20
The COORDINATION action with label NP3 calculates the following quantities:
 Quantity   
 Description  
NP3.value
the value of the coordinationNP4:  COORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=P4  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=0.6} NLIST Use a neighbor list to speed up the calculation NL_CUTOFFThe cutoff for the neighbor list=2.0 NL_STRIDEThe frequency with which we are updating the atoms in the neighbor list=20

#########################
### DEFINITION_OF_CVs ###
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# CV1: pp.proj = projection on the axis. The distance from the axis to the origin (along the axis) (biased)
# CV2: pp.ext = orthogonal distance between the ATOM(=lig) to the axis. (not biased - just monitored)
# CV4: CMAP of 5 protein-ligand contacts
# CV3: RMSD just monitored 
##############################
The COORDINATION action with label NP4 calculates the following quantities:
 Quantity   
 Description  
NP4.value
the value of the coordinationpp: PROJECTION_ON_AXISCalculate a position based on the projection along and extension from a defined axis. More details AXIS_ATOMSThe atoms that define the direction of the axis of interest=p0,p1 ATOMThe atom whose position we want to project on the axis of interest=lig

################
#RMSD WALLS ####
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The PROJECTION_ON_AXIS action with label pp calculates the following quantities:
 Quantity   
 Description  
pp.value
the value of the projection along the axisrmsd_protCA: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd_protCA calculates the following quantities:
 Quantity   
 Description  
rmsd_protCA.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputuwall_rmsd_protCA: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_protCA ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=200000

The UPPER_WALLS action with label uwall_rmsd_protCA calculates the following quantities:
 Quantity   
 Description  
uwall_rmsd_protCA.bias
the instantaneous value of the bias potential
uwall_rmsd_protCA.force2
the instantaneous value of the squared force due to this bias potentialrmsd_pocket_1: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_1.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd_pocket_1 calculates the following quantities:
 Quantity   
 Description  
rmsd_pocket_1.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputuwall_rmsd_pocket_1: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_1 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000

The UPPER_WALLS action with label uwall_rmsd_pocket_1 calculates the following quantities:
 Quantity   
 Description  
uwall_rmsd_pocket_1.bias
the instantaneous value of the bias potential
uwall_rmsd_pocket_1.force2
the instantaneous value of the squared force due to this bias potentialrmsd_pocket_2: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_2.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd_pocket_2 calculates the following quantities:
 Quantity   
 Description  
rmsd_pocket_2.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputuwall_rmsd_pocket_2: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_2 ATthe positions of the wall=0.23 KAPPAthe force constant for the wall=200000

The UPPER_WALLS action with label uwall_rmsd_pocket_2 calculates the following quantities:
 Quantity   
 Description  
uwall_rmsd_pocket_2.bias
the instantaneous value of the bias potential
uwall_rmsd_pocket_2.force2
the instantaneous value of the squared force due to this bias potentialrmsd_pocket_3: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_pocket_3.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd_pocket_3 calculates the following quantities:
 Quantity   
 Description  
rmsd_pocket_3.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputuwall_rmsd_pocket_3: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_pocket_3 ATthe positions of the wall=0.25 KAPPAthe force constant for the wall=200000

The UPPER_WALLS action with label uwall_rmsd_pocket_3 calculates the following quantities:
 Quantity   
 Description  
uwall_rmsd_pocket_3.bias
the instantaneous value of the bias potential
uwall_rmsd_pocket_3.force2
the instantaneous value of the squared force due to this bias potentialrmsd_tail: RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=../rmsd_ref_tail.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL
The RMSD action with label rmsd_tail calculates the following quantities:
 Quantity   
 Description  
rmsd_tail.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputuwall_rmsd_tail: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd_tail ATthe positions of the wall=0.4 KAPPAthe force constant for the wall=200000

##########################
### CMAP #################
##########################
The UPPER_WALLS action with label uwall_rmsd_tail calculates the following quantities:
 Quantity   
 Description  
uwall_rmsd_tail.bias
the instantaneous value of the bias potential
uwall_rmsd_tail.force2
the instantaneous value of the squared force due to this bias potentialINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=../cmap.dat
# The command:
# INCLUDE FILE=../cmap.dat
# ensures PLUMED loads the contents of the file called ../cmap.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label ../cmap.dat calculates somethingCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2124          SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2131           SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS3the atoms involved in each of the contacts you wish to calculate=932,2141           SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS4the atoms involved in each of the contacts you wish to calculate=857,2137           SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
LABELa label for the action so that its output can be referenced in the input to other actions=cmap
SUM calculate the sum of all the contacts in the input
... CONTACTMAP

The CONTACTMAP action with label cmap calculates the following quantities:
 Quantity   
 Description  
cmap.contact
By not using SUM or CMDIST each contact will be stored in a component
cmap.value
the sum of all the switching function on all the distancesCONTACTMAPCalculate the distances between a number of pairs of atoms and transform each distance by a switching function. More details ...
ATOMS1the atoms involved in each of the contacts you wish to calculate=1665,2124          SWITCH1The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS2the atoms involved in each of the contacts you wish to calculate=699,2131           SWITCH2The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS3the atoms involved in each of the contacts you wish to calculate=932,2141           SWITCH3The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
ATOMS4the atoms involved in each of the contacts you wish to calculate=857,2137           SWITCH4The switching functions to use for each of the contacts in your map. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.55 D_0=0.00 NN=4 MM=10}  
LABELa label for the action so that its output can be referenced in the input to other actions=cmappa
... CONTACTMAP
# --- End of included input --- 

##########################
# Stiff lig torsions #####
##########################

The CONTACTMAP action with label cmappa calculates the following quantities:
 Quantity   
 Description  
cmappa.contact
By not using SUM or CMDIST each contact will be stored in a component
cmappa.value
the sum of all the switching function on all the distanceslig_torsion1: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2163,2134,2122,2123
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=2147,2137,2163,2133
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=2127,2152,2149,2148

#########################
### FUNNEL_PARAMETERS ###
#########################
The TORSION action with label lig_torsion3 calculates the following quantities:
 Quantity   
 Description  
lig_torsion3.value
the TORSION involving these atomss_cent: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=2.6                              # INFLEXION
The CONSTANT action with label s_cent calculates the following quantities:
 Quantity   
 Description  
s_cent.value
the constant value that was read from the plumed inputbeta_cent: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.8                            # STEEPNESS
The CONSTANT action with label beta_cent calculates the following quantities:
 Quantity   
 Description  
beta_cent.value
the constant value that was read from the plumed inputwall_width: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.1                                  # WIDTH (h)
The CONSTANT action with label wall_width calculates the following quantities:
 Quantity   
 Description  
wall_width.value
the constant value that was read from the plumed inputwall_buffer: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=0.25                                 # BUFFER (f, total width = WIDTH + BUFFER)
The CONSTANT action with label wall_buffer calculates the following quantities:
 Quantity   
 Description  
wall_buffer.value
the constant value that was read from the plumed inputlwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=1.4 KAPPAthe force constant for the wall=2000         # Lower Wall 
The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=pp.proj ATthe positions of the wall=3.3 KAPPAthe force constant for the wall=2000     # Upper Wall 

####################################
########### CALCULATE FUNNEL #######
# Returns the radius of the funnel
# at the current value of the cv
####################################
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=wall_center
    ARGthe values input to this function=pp.proj,s_cent,beta_cent,wall_width,wall_buffer
    VARthe names to give each of the arguments in the function=s,sc,b,h,f
    FUNCthe function you wish to evaluate=h*(1./(1.+exp(b*(s-sc))))+f
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL

################################
##### POTENTIAL_PARAMETERS #####
################################
The MATHEVAL action with label wall_center calculates the following quantities:
 Quantity   
 Description  
wall_center.value
an arbitrary functionscaling: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=1.0
The CONSTANT action with label scaling calculates the following quantities:
 Quantity   
 Description  
scaling.value
the constant value that was read from the plumed inputspring: CONSTANTCreate a constant value that can be passed to actions More details VALUESthe numbers that are in your constant value=10000.0

################################
####### DEFINE_POTENTIAL #######
################################
The CONSTANT action with label spring calculates the following quantities:
 Quantity   
 Description  
spring.value
the constant value that was read from the plumed inputMATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ...
    LABELa label for the action so that its output can be referenced in the input to other actions=wall_bias
    ARGthe values input to this function=pp.ext,spring,wall_center,scaling
    VARthe names to give each of the arguments in the function=z,k,zc,sf
    FUNCthe function you wish to evaluate=step(z-zc)*k*(z-zc)*(z-zc)/(sf*sf)
    PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... MATHEVAL
The MATHEVAL action with label wall_bias calculates the following quantities:
 Quantity   
 Description  
wall_bias.value
an arbitrary functionfinalbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=wall_bias

#################################
######## DEFINE_OPES_EXPLORE ####
#################################

The BIASVALUE action with label finalbias calculates the following quantities:
 Quantity   
 Description  
finalbias.bias
the instantaneous value of the bias potential
finalbias._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileene: ENERGYCalculate the total potential energy of the simulation box. More details

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=350
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=2000 


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=pp.proj,cmap
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.07,0.15
  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
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.Kernels
  PACEthe frequency for kernel deposition=20000
  BARRIERthe free energy barrier to be overcome=30
... 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=opesNP1
  ARGthe labels of the scalars on which the bias will act=NP1,lig_torsion1,lig_torsion2
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,0.3,2.5
  FILE a file in which the list of all deposited kernels is stored=KernelsNP1.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP1
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE



The OPES_METAD_EXPLORE action with label opesNP1 calculates the following quantities:
 Quantity   
 Description  
opesNP1.bias
the instantaneous value of the bias potential
opesNP1.rct
estimate of c(t)
opesNP1.zed
estimate of Z_n
opesNP1.neff
effective sample size
opesNP1.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=opesNP2
  ARGthe labels of the scalars on which the bias will act=NP2,lig_torsion2,lig_torsion3
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,2.5,2.6
  FILE a file in which the list of all deposited kernels is stored=KernelsNP2.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP2
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opesNP2 calculates the following quantities:
 Quantity   
 Description  
opesNP2.bias
the instantaneous value of the bias potential
opesNP2.rct
estimate of c(t)
opesNP2.zed
estimate of Z_n
opesNP2.neff
effective sample size
opesNP2.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=opesNP3
  ARGthe labels of the scalars on which the bias will act=NP3,lig_torsion3,lig_torsion1
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,2.6,0.3
  FILE a file in which the list of all deposited kernels is stored=KernelsNP3.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP3
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE



The OPES_METAD_EXPLORE action with label opesNP3 calculates the following quantities:
 Quantity   
 Description  
opesNP3.bias
the instantaneous value of the bias potential
opesNP3.rct
estimate of c(t)
opesNP3.zed
estimate of Z_n
opesNP3.neff
effective sample size
opesNP3.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=opesNP4
  ARGthe labels of the scalars on which the bias will act=NP4,lig_torsion1,lig_torsion2
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.1,0.3,2.5
  FILE a file in which the list of all deposited kernels is stored=KernelsNP4.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP4
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNP4
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opesNP4 calculates the following quantities:
 Quantity   
 Description  
opesNP4.bias
the instantaneous value of the bias potential
opesNP4.rct
estimate of c(t)
opesNP4.zed
estimate of Z_n
opesNP4.neff
effective sample size
opesNP4.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=opesNG1
  ARGthe labels of the scalars on which the bias will act=NG1,lig_torsion2,lig_torsion3
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.4,2.5,2.6
  FILE a file in which the list of all deposited kernels is stored=KernelsNG1.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNG1
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNG1
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opesNG1 calculates the following quantities:
 Quantity   
 Description  
opesNG1.bias
the instantaneous value of the bias potential
opesNG1.rct
estimate of c(t)
opesNG1.zed
estimate of Z_n
opesNG1.neff
effective sample size
opesNG1.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=opesNG2
  ARGthe labels of the scalars on which the bias will act=NG2,lig_torsion3,lig_torsion1
  SIGMA the initial widths of the kernels, divided by the square root of gamma=0.2,2.6,0.3
  FILE a file in which the list of all deposited kernels is stored=KernelsNG2.data
  STATE_RFILEread from this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNG2
  STATE_WFILEwrite to this file the compressed kernels and all the info needed to RESTART the simulation=compressed.KernelsNG2
  PACEthe frequency for kernel deposition=40000
  BARRIERthe free energy barrier to be overcome=3
... OPES_METAD_EXPLORE


The OPES_METAD_EXPLORE action with label opesNG2 calculates the following quantities:
 Quantity   
 Description  
opesNG2.bias
the instantaneous value of the bias potential
opesNG2.rct
estimate of c(t)
opesNG2.zed
estimate of Z_n
opesNG2.neff
effective sample size
opesNG2.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=* 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