PLUMED-NEST

Project ID: plumID:20.018
Source: dimer/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 NATURAL use natural units

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=dist
The DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Description  
dist.value
the DISTANCE between this pair of atomsCOORDINATIONCalculate coordination numbers. More details GROUPAFirst list of atoms=1 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=2 R_0The r_0 parameter of the switching function=1.0 D_0 The d_0 parameter of the switching function=0.75 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=coord

The COORDINATION action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.value
the value of the coordinationUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=dist ATthe positions of the wall=7.0 KAPPAthe force constant for the wall=1.0 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 potentialMETADUsed to performed metadynamics on one or more collective variables. More details ...
  ARGthe labels of the scalars on which the bias will act=coord
  SIGMAthe widths of the Gaussian hills=0.01
  HEIGHTthe heights of the Gaussian hills=0.25
  PACEthe frequency for hill addition=2500
  BIASFACTORuse well tempered metadynamics and use this bias factor=10
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=1.5
  GRID_MINthe lower bounds for the grid=0.0
  GRID_MAXthe upper bounds for the grid=1.0
  GRID_BINthe number of bins for the grid=500
  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
  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_METADCalculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details TEMPthe system temperature=1.5 LABELa label for the action so that its output can be referenced in the input to other actions=bias
The REWEIGHT_METAD action with label bias calculates the following quantities:
 Quantity   
 Description  
bias.value
the weight to use for this frame to negate the effect the metadynamics biasREWEIGHT_GEOMFESThis action is not part of PLUMED and was included by using a LOAD command More details TEMP=1.5 ARG=coord LABEL=geom

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=dist
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=10.0
  GRID_BINthe number of bins for the grid=1000
  BANDWIDTHthe bandwidths for kernel density esimtation=0.05
  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=hdist
... HISTOGRAM

The HISTOGRAM action with label hdist calculates the following quantities:
 Quantity   
 Description  
hdist.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=coord
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=1.0
  GRID_BINthe number of bins for the grid=200
  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=hcoord
... HISTOGRAM

The HISTOGRAM action with label hcoord calculates the following quantities:
 Quantity   
 Description  
hcoord.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=coord
  GRID_MIN the lower bounds for the grid=0.0
  GRID_MAX the upper bounds for the grid=1.0
  GRID_BINthe number of bins for the grid=200
  BANDWIDTHthe bandwidths for kernel density esimtation=0.02
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,geom
  LABELa label for the action so that its output can be referenced in the input to other actions=hcoordg
... HISTOGRAM

The HISTOGRAM action with label hcoordg calculates the following quantities:
 Quantity   
 Description  
hcoordg.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)=hdist TEMPthe temperature at which you are operating=1.5 LABELa label for the action so that its output can be referenced in the input to other actions=fdist
The CONVERT_TO_FES action with label fdist calculates the following quantities:
 Quantity   
 Description  
fdist.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)=hcoord TEMPthe temperature at which you are operating=1.5 LABELa label for the action so that its output can be referenced in the input to other actions=fcoord
The CONVERT_TO_FES action with label fcoord calculates the following quantities:
 Quantity   
 Description  
fcoord.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)=hcoordg TEMPthe temperature at which you are operating=1.5 LABELa label for the action so that its output can be referenced in the input to other actions=fcoordg

The CONVERT_TO_FES action with label fcoordg calculates the following quantities:
 Quantity   
 Description  
fcoordg.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)=fdist FILE the file on which to write the grid=fesdist STRIDE the frequency with which the grid should be output to the file=500000
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)=fcoord FILE the file on which to write the grid=fescoord STRIDE the frequency with which the grid should be output to the file=500000
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)=fcoordg FILE the file on which to write the grid=fescoordg STRIDE the frequency with which the grid should be output to the file=500000

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=10000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dist,coord,b1.bias,b1.rct STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=colvar