PLUMED-NEST-TEST-SITE

Project ID: plumID:19.071
Source: MFI_paper_scripts/reweighting/plumed_REWE.dat
Originally used with PLUMED version: 2.4
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

p: READRead quantities from a colvar file. More details  FILEthe name of the file from which to read these quantities=./position  VALUESthe values to read from the file=p.x IGNORE_FORCES use this flag if the forces added by any bias can be safely ignored IGNORE_TIME ignore the time in the colvar file

The READ action with label p calculates the following quantities:
 Quantity   
 Description  
p..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsMETADUsed to performed metadynamics on one or more collective variables. More details ... 
ARGthe labels of the scalars on which the bias will act=p.x
SIGMAthe widths of the Gaussian hills=0.05 
HEIGHTthe heights of the Gaussian hills=0.1 
PACEthe frequency for hill addition=500 
BIASFACTORuse well tempered metadynamics and use this bias factor=5 
LABELa label for the action so that its output can be referenced in the input to other actions=metad 
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=120
GRID_MINthe lower bounds for the grid=-2.6
GRID_MAXthe upper bounds for the grid=2.6
GRID_BINthe number of bins for the grid=500 
REWEIGHTING_NGRID=200 
REWEIGHTING_NHILLS=10
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialbias: 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=120

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 biasHISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
  ARGthe quantities that are being used to construct the histogram=p.x
  GRID_MIN the lower bounds for the grid=-2.6
  GRID_MAX the upper bounds for the grid=2.6
  GRID_BINthe number of bins for the grid=500
  BANDWIDTHthe bandwidths for kernel density esimtation=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=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 obtainedff: CONVERT_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=120 


The CONVERT_TO_FES action with label ff calculates the following quantities:
 Quantity   
 Description  
ff.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=500