PLUMED-NEST

Project ID: plumID:23.001
Source: EnhancedCoexistence/Liq-III/5-BiasedCoexistence/COEX_2000.0atm/225.0K/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=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 


INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=plumed.order.dat
# The command:
# INCLUDE FILE=plumed.order.dat
# ensures PLUMED loads the contents of the file called plumed.order.dat
# The contents of this file are shown below (click the red comment to hide them).
#Minimum overlap for sigma = 0.065
#Liquid max: 0.535
#Ice max: 0.9625
#Midpoint between distribitions: 0.745


#Smooth counting of ice molecules
The INCLUDE action with label plumed.order.dat calculates something
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
=1-2268:3
 
SIGMA
 the width to use for the gaussian kernels
=0.065
 
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
=refcvThe CUSTOM action with label refcv calculates the following quantities:
 Quantity   
 Type   
 Description  
refcv
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors
 
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_THAN1
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.535 D_MAX=0.925}
 
MORE_THAN2
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.745000 D_MAX=0.745001}	
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# --- End of included input --- 
# Use wall potential too keep colective variable within limits
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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-1 
AT
the positions of the wall
=405 
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
=2
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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-1 
AT
the positions of the wall
=351 
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
=2



PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=500  
ARG
the labels of the values that you would like to print to the file
 
FILE
the name of the file on which to output these quantities
=COLVAR-EQUILIBRATE