PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-275.0-3000.0/plumed.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. 

RESTART
Activate restart. More details
 
NO
 switch off restart - can be used to override the behavior of the MD engine

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

# Target uniform distribution of the order parameter between 324 and 378 molecules
# i.e. between 6 and 7 (half)layers, each of 54 molecules
umb1: 
ECV_UMBRELLAS_LINE
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=refcv.morethan 
TEMP
 temperature
=290 
CV_MIN
the minimum of the CV range to be explored
=324.0 
CV_MAX
the maximum of the CV range to be explored
=378.0 
SIGMA
sigma of the umbrella Gaussians
=1 
BARRIER
a guess of the free energy barrier to be overcome (better to stay higher than lower)
=100
The ECV_UMBRELLAS_LINE action with label umb1 calculates a scalar quantityopes: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details
 
ARG
the label of the ECVs that define the expansion
=umb1 
PACE
how often the bias is updated
=500 
STRIDE
the frequency with which the forces due to the bias should be calculated
=3 
WALKERS_MPI
 switch on MPI version of multiple walkers

The OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
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