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=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

ENVIRONMENTSIMILARITY
Measure how similar the environment around atoms is to that found in some reference crystal structure. More details
 ...
 
SPECIES
this 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
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=refcv
 
REFERENCE_1
PDB files with relative distances from central atom
=env1.pdb
 
REFERENCE_2
PDB files with relative distances from central atom
=env2.pdb
 
REFERENCE_3
PDB files with relative distances from central atom
=env3.pdb
 
REFERENCE_4
PDB files with relative distances from central atom
=env4.pdb
 
REFERENCE_5
PDB files with relative distances from central atom
=env5.pdb
 
REFERENCE_6
PDB files with relative distances from central atom
=env6.pdb
 
REFERENCE_7
PDB files with relative distances from central atom
=env7.pdb
 
REFERENCE_8
PDB files with relative distances from central atom
=env8.pdb
 
REFERENCE_9
PDB files with relative distances from central atom
=env9.pdb
 
REFERENCE_10
PDB files with relative distances from central atom
=env10.pdb
 
REFERENCE_11
PDB files with relative distances from central atom
=env11.pdb
 
REFERENCE_12
PDB files with relative distances from central atom
=env12.pdb
 
MORE_THAN
calculate 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: 
HISTOGRAM
Accumulate the average probability density along a few CVs from a trajectory. More details
 ...
   
DATA
an 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_BIN
the number of bins for the grid
=1000
   
BANDWIDTH
the 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 obtained
DUMPGRID
Output the function on the grid to a file with the PLUMED grid format. More details
 
GRID
the 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 something
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=COLVAR