PLUMED-NEST

Project ID: plumID:21.009
Source: npt-fes/plumed.inp
Originally used with PLUMED version: 2.6
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A

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

COORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=coord
  SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-512
  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.={RATIONAL R_0=5.0 D_MAX=10.0}
  MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0 D_MAX=5.5}
  LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

The COORDINATIONNUMBER action with label coord calculates the following quantities:
 Quantity   
 Description  
coord.morethan
the number of colvars that have a value more than a threshold
coord.value
the coordination numbers of the specified atomsCOORDINATIONNUMBERCalculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details ...
  LABELa label for the action so that its output can be referenced in the input to other actions=coord1
  SPECIESthe list of atoms for which the symmetry function is being calculated and the atoms that can be in the environments=1-512
  R_0The r_0 parameter of the switching function=5.0
  MORE_THANcalculate the number of variables that are more than a certain target value. Options for this keyword are explained in the documentation for MORE_THAN.={RATIONAL R_0=5.0 D_MAX=5.5}
  MOMENTSthe list of moments that you would like to calculate=2,3
  LOWMEM this flag does nothing and is present only to ensure back-compatibility
... COORDINATIONNUMBER

The COORDINATIONNUMBER action with label coord1 calculates the following quantities:
 Quantity   
 Description  
coord1.morethan
the number of colvars that have a value more than a threshold
coord1.moment
the moments of the distribution
coord1.value
the coordination numbers of the specified atomsUPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=coord.morethan ATthe positions of the wall=64 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=wall

The UPPER_WALLS action with label wall calculates the following quantities:
 Quantity   
 Description  
wall.bias
the instantaneous value of the bias potential
wall.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.morethan
  SIGMAthe widths of the Gaussian hills=5000
  ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF
  SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.025
  SIGMA_MAXthe upper bounds for the sigmas (in CV units) when using adaptive hills=5.000
  HEIGHTthe heights of the Gaussian hills=0.5
  PACEthe frequency for hill addition=10000
  BIASFACTORuse well tempered metadynamics and use this bias factor=15
  TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=80.7
  GRID_MINthe lower bounds for the grid=0.0
  GRID_MAXthe upper bounds for the grid=140.0
  GRID_BINthe number of bins for the grid=14000
  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=40
  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=80.7 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=80.7 ARG=coord.morethan LABEL=gd1

HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=coord.morethan
  GRID_MIN the lower bounds for the grid=-0.2
  GRID_MAX the upper bounds for the grid=64
  GRID_BINthe number of bins for the grid=6420
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias
  CLEAR the frequency with whihc to clear the data that is being averaged=40000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hh
... HISTOGRAM

The HISTOGRAM action with label hh calculates the following quantities:
 Quantity   
 Description  
hh.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.morethan
  GRID_MIN the lower bounds for the grid=-0.2
  GRID_MAX the upper bounds for the grid=64
  GRID_BINthe number of bins for the grid=6420
  BANDWIDTHthe bandwidths for kernel density esimtation=0.1
  LOGWEIGHTSthe logarithm of the quantity to use as the weights when calculating averages=bias,gd1
  CLEAR the frequency with whihc to clear the data that is being averaged=40000000
  LABELa label for the action so that its output can be referenced in the input to other actions=hhg
... HISTOGRAM

The HISTOGRAM action with label hhg calculates the following quantities:
 Quantity   
 Description  
hhg.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)=hh  TEMPthe temperature at which you are operating=80.7 LABELa label for the action so that its output can be referenced in the input to other actions=ff
The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.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)=hhg TEMPthe temperature at which you are operating=80.7 LABELa label for the action so that its output can be referenced in the input to other actions=ffg

The CONVERT_TO_FES action with label ffg calculates the following quantities:
 Quantity   
 Description  
ffg.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)=ff  FILE the file on which to write the grid=fes  STRIDE the frequency with which the grid should be output to the file=40000000
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)=ffg FILE the file on which to write the grid=fesg STRIDE the frequency with which the grid should be output to the file=40000000

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=200000
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=coord.morethan,coord1.morethan,coord1.moment-2,coord1.moment-3,b1.bias STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=colvar