PLUMED-NEST

Project ID: plumID:23.001
Source: EnhancedCoexistence/Liq-VI/4-BiasedCoexistence/COEX_7000.0atm/245.0K/plumed.start.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).
#7000atm_255K
#sigma: 0.055
#Liquid max: 0.46
#Ice max: 0.9325
#Midpoint between distribitions: 0.7275

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
=1-3840:3
 
SIGMA
 the width to use for the gaussian kernels
=0.055
 
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
 
MORE_THAN1
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.46 D_MAX=0.9325}
 
MORE_THAN2
calculate the number of variables that are more than a certain target value
={CUBIC D_0=0.72750 D_MAX=0.72751}
 
MEAN
 calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# --- End of included input --- 
# Target uniform distribution of the order parameter between 640 and 720 molecules
# i.e. between 8 and 9 (half)layers, each of 80 molecules
umb1The ECV_UMBRELLAS_LINE action with label umb1 calculates the following quantities:
 Quantity   
 Type   
 Description  
umb1.refcv_morethan-1
scalar
the value of the argument named refcv_morethan-1: 
ECV_UMBRELLAS_LINE
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action has hidden defaults. More details
 
ARG
the labels of the scalar values that are input to this action
=refcv.morethan-1 
TEMP
 temperature
=245.0 
CV_MIN
the minimum of the CV range to be explored
=640.0 
CV_MAX
the maximum of the CV range to be explored
=720.0 
SIGMA
sigma of the umbrella Gaussians
=1 
BARRIER
a guess of the free energy barrier to be overcome (better to stay higher than lower)
=50
umb1: 
ECV_UMBRELLAS_LINE
Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location. This action uses the defaults shown here. More details
 
ARG
the labels of the scalar values that are input to this action
=refcv.morethan-1 
TEMP
 temperature
=245.0 
CV_MIN
the minimum of the CV range to be explored
=640.0 
CV_MAX
the maximum of the CV range to be explored
=720.0 
SIGMA
sigma of the umbrella Gaussians
=1 
BARRIER
a guess of the free energy barrier to be overcome (better to stay higher than lower)
=50  
SPACING
 the distance between umbrellas, in units of SIGMA
=1
opesThe OPES_EXPANDED action with label opes calculates the following quantities:
 Quantity   
 Type   
 Description  
opes.bias
scalar
the instantaneous value of the bias potential: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action has hidden defaults. More details
 
ARG
the label of the ECVs that define the expansion
=umb1 
PACE
how often the bias is updated
=2000 
STRIDE
the frequency with which the forces due to the bias should be calculated
=1 
WALKERS_MPI
 switch on MPI version of multiple walkers
 
opes: 
OPES_EXPANDED
On-the-fly probability enhanced sampling with expanded ensembles for the target distribution. This action uses the defaults shown here. More details
 
ARG
the label of the ECVs that define the expansion
=umb1 
PACE
how often the bias is updated
=2000 
STRIDE
the frequency with which the forces due to the bias should be calculated
=1 
WALKERS_MPI
 switch on MPI version of multiple walkers
  
OBSERVATION_STEPS
 number of unbiased initial PACE steps to collect statistics for initialization
=100 
FILE
 a file with the estimate of the relative Delta F for each component of the target and of the global c(t)
=DELTAFS 
PRINT_STRIDE
 stride for printing to DELTAFS file, in units of PACE
=100



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