PLUMED-NEST

Project ID: plumID:22.021
Source: IceIII-Liquid/5-BiasedCoexistence/COEX_2000.0atm/270.0K/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=plumedEnables syntax highlighting for PLUMED files in vim. See here for more details. 


INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed.smooth.dat
# The command:
# INCLUDE FILE=plumed.smooth.dat
# ensures PLUMED loads the contents of the file called plumed.smooth.dat
# The contents of this file are shown below (click the red comment to hide them).

#Smooth counting of ice molecules
The INCLUDE action with label plumed.smooth.dat 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=1-2268:3
 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=0.6075 D_MAX=0.9675}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# --- End of included input --- 
# Use wall potential too keep colective variable within limits
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 colvarsuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=refcv.morethan ATthe positions of the wall=405. KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=2
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentiallwall: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=refcv.morethan ATthe positions of the wall=351. KAPPAthe force constant for the wall=1.0 EXP the powers for the walls=2 STRIDEthe frequency with which the forces due to the bias should be calculated=2

The LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Description  
lwall.bias
the instantaneous value of the bias potential
lwall.force2
the instantaneous value of the squared force due to this bias potentialINCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed.strict.dat
# The command:
# INCLUDE FILE=plumed.strict.dat
# ensures PLUMED loads the contents of the file called plumed.strict.dat
# The contents of this file are shown below (click the red comment to hide them).


# Strict counting of molecules
The INCLUDE action with label plumed.strict.dat 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=1-2268:3
 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=0.7675 D_MAX=0.7675001}
 MEAN calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# --- End of included input --- 
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 threshold
refcv2.mean
the mean of the colvarsPRINTPrint 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-EQUILIBRATE