Project ID: plumID:22.016
Source: SurfaceFreeEnergy/FindOptimalParameters/FindOptimalOrderParameter-SmallEnv/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
tested onv2.9
tested onmaster
# 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
=env1h.pdb
REFERENCE_2
PDB files with relative distances from central atom
=env2h.pdb
REFERENCE_3
PDB files with relative distances from central atom
=env3h.pdb
REFERENCE_4
PDB files with relative distances from central atom
=env4h.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
hh:
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 ...
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
STRIDE
the frequency with which the grid should be output to the file
=100
PRINT
Print quantities to a file. More details
STRIDE
the frequency with which the quantities of interest should be output
=500
ARG
the input for this action is the scalar output from one or more other actions
FILE
the name of the file on which to output these quantities
=COLVAR