PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/1-distributions/3000bar-295K/CalculateOptimalSigma/Liquid/plumed-base.dat
Originally used with PLUMED version: 2.8
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

# vim:ft=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

ENVIRONMENTSIMILARITYMeasure how similar the environment around atoms is to that found in some reference crystal structure. More details ...
 SPECIESthis keyword is used for colvars such as coordination number=1-864:3
 SIGMA the width to use for the gaussian kernels=1. #replace
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv
 REFERENCE_1PDB files with relative distances from central atom=env1.pdb
 REFERENCE_2PDB files with relative distances from central atom=env2.pdb
 REFERENCE_3PDB files with relative distances from central atom=env3.pdb
 REFERENCE_4PDB files with relative distances from central atom=env4.pdb
 REFERENCE_5PDB files with relative distances from central atom=env5.pdb
 REFERENCE_6PDB files with relative distances from central atom=env6.pdb
 REFERENCE_7PDB files with relative distances from central atom=env7.pdb
 REFERENCE_8PDB files with relative distances from central atom=env8.pdb
 REFERENCE_9PDB files with relative distances from central atom=env9.pdb
 REFERENCE_10PDB files with relative distances from central atom=env10.pdb
 REFERENCE_11PDB files with relative distances from central atom=env11.pdb
 REFERENCE_12PDB files with relative distances from central atom=env12.pdb
 MORE_THANcalculate the number of variables that are more than a certain target value={RATIONAL R_0=0.5 NN=8 MM=16}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY

The ENVIRONMENTSIMILARITY action with label refcv calculates the following quantities:
 Quantity   
 Description  
refcv.value
the environmental similar parameter for each of the input atoms
refcv.morethan
the number of colvars that have a value more than a threshold
refcv.mean
the mean of the colvarshh: HISTOGRAMAccumulate the average probability density along a few CVs from a trajectory. More details ...
   DATAan alternative to the ARG keyword=refcv
   GRID_MIN the lower bounds for the grid=-0.5
   GRID_MAX the upper bounds for the grid=2
   GRID_BINthe number of bins for the grid=1000
   BANDWIDTHthe bandwidths for kernel density esimtation=0.01
...

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 obtainedDUMPGRIDOutput 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)=hh FILE the file on which to write the grid=histo

The DUMPGRID action with label  calculates somethingPRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500  ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR