PLUMED-NEST

Project ID: plumID:23.004
Source: BiasedCoexistence/IceIII/3-production/IceIII-265.0-3000.0/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 

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

The RESTART action with label  calculates somethingENVIRONMENTSIMILARITYMeasure 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=1-1944:3
 SIGMA the width to use for the gaussian kernels=0.0675
 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. Options for this keyword are explained in the documentation for MORE_THAN.={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
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 thresholdumb1: ECV_UMBRELLAS_LINETarget a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. More details ARGthe labels of the scalar values that are input to this action=refcv.morethan TEMP temperature=290 CV_MINthe minimum of the CV range to be explored=324.0 CV_MAXthe maximum of the CV range to be explored=378.0 SIGMAsigma of the umbrella Gaussians=1 BARRIERa 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 the following quantities:
 Quantity   
 Description  
umb1..#!custom
the names of the output components for this action depend on the actions input file see the example inputs below for detailsopes: OPES_EXPANDEDOn-the-fly probability enhanced sampling with expanded ensembles for the target distribution. More details ARGthe label of the ECVs that define the expansion=umb1.* PACEhow often the bias is updated=500 STRIDEthe 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 potentialENVIRONMENTSIMILARITYMeasure 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=1-1944:3
 SIGMA the width to use for the gaussian kernels=0.0675
 CRYSTAL_STRUCTURE Targeted crystal structure=CUSTOM
 LABELa label for the action so that its output can be referenced in the input to other actions=refcv2
 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. Options for this keyword are explained in the documentation for MORE_THAN.={CUBIC D_0=0.763000 D_MAX=0.763001}
... ENVIRONMENTSIMILARITY

The ENVIRONMENTSIMILARITY action with label refcv2 calculates the following quantities:
 Quantity   
 Description  
refcv2.value
the environmental similar parameter for each of the input atoms
refcv2.morethan
the number of colvars that have a value more than a thresholdPRINTPrint 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