PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-265.0-3000.0/plumed.equil.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
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
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
={CUBIC D_0=0.604 D_MAX=0.972}
... ENVIRONMENTSIMILARITY

# Restraint
lwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=refcv.morethan 
AT
the positions of the wall
=324 
KAPPA
the force constant for the wall
=1.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=5
uwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=refcv.morethan 
AT
the positions of the wall
=378 
KAPPA
the force constant for the wall
=1.0 
EXP
 the powers for the walls
=2 
STRIDE
the frequency with which the forces due to the bias should be calculated
=5

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
=1-1944:3
 
SIGMA
 the width to use for the gaussian kernels
=0.0675
 
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
=refcv2
 
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
={CUBIC D_0=0.763000 D_MAX=0.763001}
... ENVIRONMENTSIMILARITY

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.EQUIL