PLUMED-NEST

Project ID: plumID:20.018
Source: da-wt/plumed.inp
Originally used with PLUMED version: 2.6-mod
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

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=fs ENERGYthe units of energy=kcal/mol

The UNITS action with label  calculates somethingLOADLoads a library, possibly defining new actions. More details FILEfile to be loaded=../src/bias/ReweightGeomFES.cpp

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 LABELa label for the action so that its output can be referenced in the input to other actions=d1
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,3 LABELa label for the action so that its output can be referenced in the input to other actions=d2
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3,4 LABELa label for the action so that its output can be referenced in the input to other actions=d3
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=4,5 LABELa label for the action so that its output can be referenced in the input to other actions=d4
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5,6 LABEla label for the action so that its output can be referenced in the input to other actions=d5
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,6 LABELa label for the action so that its output can be referenced in the input to other actions=d6

The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=4 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5 D_0 The d_0 parameter of the switching function=1.0 R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=cn1
The COORDINATION action with label cn1 calculates the following quantities:
 Quantity   
 Description  
cn1.value
the value of the coordinationCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=6 D_0 The d_0 parameter of the switching function=1.0 R_0The r_0 parameter of the switching function=1.0 NN The n parameter of the switching function =1 LABELa label for the action so that its output can be referenced in the input to other actions=cn2

The COORDINATION action with label cn2 calculates the following quantities:
 Quantity   
 Description  
cn2.value
the value of the coordinationDENSITYDepreciated command that is bascially equivalant to GROUP. More details SPECIESthe atoms in the group=5,6 LABELa label for the action so that its output can be referenced in the input to other actions=ethylene
The DENSITY action with label ethylene calculates the following quantities:
 Quantity   
 Description  
ethylene.value
indices for the specified group of atomsDENSITYDepreciated command that is bascially equivalant to GROUP. More details SPECIESthe atoms in the group=1-4 LABELa label for the action so that its output can be referenced in the input to other actions=diene

The DENSITY action with label diene calculates the following quantities:
 Quantity   
 Description  
diene.value
indices for the specified group of atomsCENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1-4 LABELa label for the action so that its output can be referenced in the input to other actions=mol1
The CENTER action with label mol1 calculates the following quantities:
 Quantity   
 Description  
mol1.value
the position of the center of massCENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=5-6 LABELa label for the action so that its output can be referenced in the input to other actions=mol2

The CENTER action with label mol2 calculates the following quantities:
 Quantity   
 Description  
mol2.value
the position of the center of massCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ...
  ATOMSthe atoms for which you would like to calculate the adjacency matrix=ethylene,diene
  SWITCH11the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.65}
  SWITCH12the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.65}
  SWITCH22the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.65}
  LABELa label for the action so that its output can be referenced in the input to other actions=mat1
... CONTACT_MATRIX

The CONTACT_MATRIX action with label mat1 calculates the following quantities:
 Quantity   
 Description  
mat1.value
a matrix containing the weights for the bonds between each pair of atomsCONTACT_MATRIXAdjacency matrix in which two atoms are adjacent if they are within a certain cutoff. More details ...
  ATOMSthe atoms for which you would like to calculate the adjacency matrix=ethylene,diene
  SWITCH11the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  SWITCH12the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  SWITCH22the input for the switching function that acts upon the distance between each pair of atoms. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL D_0=0.0 R_0=2.12 NN=24}
  LABELa label for the action so that its output can be referenced in the input to other actions=mat2
... CONTACT_MATRIX

The CONTACT_MATRIX action with label mat2 calculates the following quantities:
 Quantity   
 Description  
mat2.value
a matrix containing the weights for the bonds between each pair of atomsCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details SPECIESAthe list of atoms for which the symmetry function is being calculated=ethylene SPECIESBthe list of atoms that can be in the environments of each of the atoms for which the symmetry function is being calculated=diene MEAN calculate the mean of all the quantities SWITCHthe switching function that it used in the construction of the contact matrix. Options for this keyword are explained in the documentation for LESS_THAN.={GAUSSIAN D_0=1.8 R_0=0.3} LABELa label for the action so that its output can be referenced in the input to other actions=cn

The COORDINATIONNUMBER action with label cn calculates the following quantities:
 Quantity   
 Description  
cn.mean
the mean of the colvars
cn.value
the coordination numbers of the specified atomsSPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=mat1 LABELa label for the action so that its output can be referenced in the input to other actions=ss1
The SPRINT action with label ss1 calculates the following quantities:
 Quantity   
 Description  
ss1.coord
the sprint coordinatesSPRINTCalculate SPRINT topological variables from an adjacency matrix. More details MATRIXthe matrix that you would like to perform SPRINT on=mat2 LABELa label for the action so that its output can be referenced in the input to other actions=ss2
The SPRINT action with label ss2 calculates the following quantities:
 Quantity   
 Description  
ss2.coord
the sprint coordinatesDISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=mol1,mol2 LABELa label for the action so that its output can be referenced in the input to other actions=dist
The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atomsCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=d1,d2,d3,d4,d6 COEFFICIENTS the coefficients of the arguments in your function=-0.05,0.21,-0.08,0.69,0.69 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=hlda
The COMBINE action with label hlda calculates the following quantities:
 Quantity   
 Description  
hlda.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=cn1,cn2 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=simple
The COMBINE action with label simple calculates the following quantities:
 Quantity   
 Description  
simple.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ss1.coord-0,ss1.coord-1 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=sprnt1
The COMBINE action with label sprnt1 calculates the following quantities:
 Quantity   
 Description  
sprnt1.value
a linear compbinationCOMBINECalculate a polynomial combination of a set of other variables. More details ARGthe values input to this function=ss2.coord-0,ss2.coord-1 COEFFICIENTS the coefficients of the arguments in your function=0.5,0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=sprnt2

The COMBINE action with label sprnt2 calculates the following quantities:
 Quantity   
 Description  
sprnt2.value
a linear compbinationUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d4,d6 ATthe positions of the wall=5.0,5.0 KAPPAthe force constant for the wall=50,50 LABELa label for the action so that its output can be referenced in the input to other actions=walls
The UPPER_WALLS action with label walls calculates the following quantities:
 Quantity   
 Description  
walls.bias
the instantaneous value of the bias potential
walls.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 ARGthe arguments on which the bias is acting=dist,sprnt1,sprnt2,cn.mean,simple ATthe positions of the wall=0,0,0,0,0 KAPPAthe force constant for the wall=50,50,50,50,50 LABELa label for the action so that its output can be referenced in the input to other actions=fake

The LOWER_WALLS action with label fake calculates the following quantities:
 Quantity   
 Description  
fake.bias
the instantaneous value of the bias potential
fake.force2
the instantaneous value of the squared force due to this bias potentialMETADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=hlda
  SIGMAthe widths of the Gaussian hills=0.15
  HEIGHTthe heights of the Gaussian hills=1.0
  PACEthe frequency for hill addition=1000
  BIASFACTORuse well tempered metadynamics and use this bias factor=25
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=600
  GRID_MINthe lower bounds for the grid=1.0
  GRID_MAXthe upper bounds for the grid=9.0
  GRID_BINthe number of bins for the grid=1600
  CALC_RCT calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  RCT_USTRIDEthe update stride for calculating the c(t) reweighting factor=1
  RESTARTallows per-action setting of restart (YES/NO/AUTO)=YES
  LABELa label for the action so that its output can be referenced in the input to other actions=b1
... METAD

The METAD action with label b1 calculates the following quantities:
 Quantity   
 Description  
b1.bias
the instantaneous value of the bias potential
b1.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
b1.rct
the reweighting factor c(t)REWEIGHT_BIASCalculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored More details    ARG the biases that must be taken into account when reweighting=b1.bias TEMPthe system temperature=600 LABELa label for the action so that its output can be referenced in the input to other actions=bias
The REWEIGHT_BIAS action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the biasREWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=d4      TEMP=600 LABEL=gd4
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=hlda    TEMP=600 LABEL=ghlda
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=sprnt1  TEMP=600 LABEL=gsprnt1
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=sprnt2  TEMP=600 LABEL=gsprnt2
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=cn.mean TEMP=600 LABEL=gcn
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=simple  TEMP=600 LABEL=gsimple
REWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details ARG=d4,d6   TEMP=600 LABEL=g2d

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4         GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=6.0         GRID_BINthe number of bins for the grid=2000    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=hd4
The HISTOGRAM action with label hd4 calculates the following quantities:
 Quantity   
 Description  
hd4.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=hlda       GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=9.0         GRID_BINthe number of bins for the grid=4000    BANDWIDTHthe bandwidths for kernel density esimtation=0.01      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=hhlda
The HISTOGRAM action with label hhlda calculates the following quantities:
 Quantity   
 Description  
hhlda.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=sprnt1     GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=4.0         GRID_BINthe number of bins for the grid=2000    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=hsprnt1
The HISTOGRAM action with label hsprnt1 calculates the following quantities:
 Quantity   
 Description  
hsprnt1.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=sprnt2     GRID_MIN the lower bounds for the grid=-0.1 GRID_MAX the upper bounds for the grid=2.4        GRID_BINthe number of bins for the grid=2500    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=hsprnt2
The HISTOGRAM action with label hsprnt2 calculates the following quantities:
 Quantity   
 Description  
hsprnt2.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=simple     GRID_MIN the lower bounds for the grid=0.1 GRID_MAX the upper bounds for the grid=0.8         GRID_BINthe number of bins for the grid=3500    BANDWIDTHthe bandwidths for kernel density esimtation=0.001     LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=hsimple
The HISTOGRAM action with label hsimple calculates the following quantities:
 Quantity   
 Description  
hsimple.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4,d6      GRID_MIN the lower bounds for the grid=1.0,1.0 GRID_MAX the upper bounds for the grid=2.0,2.0 GRID_BINthe number of bins for the grid=100,100 BANDWIDTHthe bandwidths for kernel density esimtation=0.04,0.04 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=h2db
The HISTOGRAM action with label h2db calculates the following quantities:
 Quantity   
 Description  
h2db.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4,d6      GRID_MIN the lower bounds for the grid=2.0,2.0 GRID_MAX the upper bounds for the grid=6.0,6.0 GRID_BINthe number of bins for the grid=80,80   BANDWIDTHthe bandwidths for kernel density esimtation=0.20,0.20 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=h2dd
The HISTOGRAM action with label h2dd calculates the following quantities:
 Quantity   
 Description  
h2dd.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4,d6      GRID_MIN the lower bounds for the grid=2.0,2.0 GRID_MAX the upper bounds for the grid=2.2,2.2 GRID_BINthe number of bins for the grid=100,100 BANDWIDTHthe bandwidths for kernel density esimtation=0.02,0.02 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias LABELa label for the action so that its output can be referenced in the input to other actions=h2d
The HISTOGRAM action with label h2d calculates the following quantities:
 Quantity   
 Description  
h2d.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4         GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=6.0         GRID_BINthe number of bins for the grid=2000    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gd4     LABELa label for the action so that its output can be referenced in the input to other actions=hd4g
The HISTOGRAM action with label hd4g calculates the following quantities:
 Quantity   
 Description  
hd4g.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=hlda       GRID_MIN the lower bounds for the grid=1.0 GRID_MAX the upper bounds for the grid=9.0         GRID_BINthe number of bins for the grid=4000    BANDWIDTHthe bandwidths for kernel density esimtation=0.01      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,ghlda   LABELa label for the action so that its output can be referenced in the input to other actions=hhldag
The HISTOGRAM action with label hhldag calculates the following quantities:
 Quantity   
 Description  
hhldag.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=sprnt1     GRID_MIN the lower bounds for the grid=0.0 GRID_MAX the upper bounds for the grid=4.0         GRID_BINthe number of bins for the grid=2000    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gsprnt1 LABELa label for the action so that its output can be referenced in the input to other actions=hsprnt1g
The HISTOGRAM action with label hsprnt1g calculates the following quantities:
 Quantity   
 Description  
hsprnt1g.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=sprnt2     GRID_MIN the lower bounds for the grid=-0.1 GRID_MAX the upper bounds for the grid=2.4        GRID_BINthe number of bins for the grid=2500    BANDWIDTHthe bandwidths for kernel density esimtation=0.02      LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gsprnt2 LABELa label for the action so that its output can be referenced in the input to other actions=hsprnt2g
The HISTOGRAM action with label hsprnt2g calculates the following quantities:
 Quantity   
 Description  
hsprnt2g.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=simple     GRID_MIN the lower bounds for the grid=0.1 GRID_MAX the upper bounds for the grid=0.8         GRID_BINthe number of bins for the grid=3500    BANDWIDTHthe bandwidths for kernel density esimtation=0.001     LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gsimple LABELa label for the action so that its output can be referenced in the input to other actions=hsimpleg
The HISTOGRAM action with label hsimpleg calculates the following quantities:
 Quantity   
 Description  
hsimpleg.value
the estimate of the histogram as a function of the argument that was obtainedHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ARGthe quantities that are being used to construct the histogram=d4,d6      GRID_MIN the lower bounds for the grid=2.0,2.0 GRID_MAX the upper bounds for the grid=2.2,2.2 GRID_BINthe number of bins for the grid=100,100 BANDWIDTHthe bandwidths for kernel density esimtation=0.02,0.02 LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,g2d     LABELa label for the action so that its output can be referenced in the input to other actions=h2dg

The HISTOGRAM action with label h2dg calculates the following quantities:
 Quantity   
 Description  
h2dg.value
the estimate of the histogram as a function of the argument that was obtainedCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hd4       TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fd4
The CONVERT_TO_FES action with label fd4 calculates the following quantities:
 Quantity   
 Description  
fd4.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hhlda     TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fhlda
The CONVERT_TO_FES action with label fhlda calculates the following quantities:
 Quantity   
 Description  
fhlda.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsprnt1   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsprnt1
The CONVERT_TO_FES action with label fsprnt1 calculates the following quantities:
 Quantity   
 Description  
fsprnt1.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsprnt2   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsprnt2
The CONVERT_TO_FES action with label fsprnt2 calculates the following quantities:
 Quantity   
 Description  
fsprnt2.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsimple   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsimple
The CONVERT_TO_FES action with label fsimple calculates the following quantities:
 Quantity   
 Description  
fsimple.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=h2db      TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=f2db
The CONVERT_TO_FES action with label f2db calculates the following quantities:
 Quantity   
 Description  
f2db.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=h2dd      TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=f2dd
The CONVERT_TO_FES action with label f2dd calculates the following quantities:
 Quantity   
 Description  
f2dd.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=h2d       TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=f2d
The CONVERT_TO_FES action with label f2d calculates the following quantities:
 Quantity   
 Description  
f2d.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hd4g       TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fd4g
The CONVERT_TO_FES action with label fd4g calculates the following quantities:
 Quantity   
 Description  
fd4g.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hhldag     TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fhldag
The CONVERT_TO_FES action with label fhldag calculates the following quantities:
 Quantity   
 Description  
fhldag.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsprnt1g   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsprnt1g
The CONVERT_TO_FES action with label fsprnt1g calculates the following quantities:
 Quantity   
 Description  
fsprnt1g.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsprnt2g   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsprnt2g
The CONVERT_TO_FES action with label fsprnt2g calculates the following quantities:
 Quantity   
 Description  
fsprnt2g.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=hsimpleg   TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=fsimpleg
The CONVERT_TO_FES action with label fsimpleg calculates the following quantities:
 Quantity   
 Description  
fsimpleg.value
the free energy surfaceCONVERT_TO_FESConvert a histogram to a free energy surface. More details GRIDthe histogram that you would like to convert into a free energy surface (old syntax)=h2dg       TEMPthe temperature at which you are operating=600 LABELa label for the action so that its output can be referenced in the input to other actions=f2dg

The CONVERT_TO_FES action with label f2dg calculates the following quantities:
 Quantity   
 Description  
f2dg.value
the free energy surfaceDUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fd4     FILE the file on which to write the grid=fesd4     STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fhlda   FILE the file on which to write the grid=feshlda   STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsprnt1 FILE the file on which to write the grid=fessprnt1 STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsprnt2 FILE the file on which to write the grid=fessprnt2 STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsimple FILE the file on which to write the grid=fessimple STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=f2db    FILE the file on which to write the grid=fes2db    STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=f2dd    FILE the file on which to write the grid=fes2dd    STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=f2d     FILE the file on which to write the grid=fes2d     STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fd4g     FILE the file on which to write the grid=fesd4g     STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fhldag   FILE the file on which to write the grid=feshldag   STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsprnt1g FILE the file on which to write the grid=fessprnt1g STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsprnt2g FILE the file on which to write the grid=fessprnt2g STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=fsimpleg FILE the file on which to write the grid=fessimpleg STRIDE the frequency with which the grid should be output to the file=5000000
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details GRIDthe grid you would like to print (can also use ARG for specifying what is being printed)=f2dg     FILE the file on which to write the grid=fes2dg     STRIDE the frequency with which the grid should be output to the file=5000000

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=2000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d4,d6,hlda,dist,cn.mean,sprnt1,sprnt2,b1.bias,b1.rct STRIDE the frequency with which the quantities of interest should be output=200 FILEthe name of the file on which to output these quantities=colvar