Project ID: plumID:21.002
Source: Crystallization/IceIc/64molecules/Multithermal/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
tested onv2.9
tested onmaster
#SETTINGS NREPLICAS=2
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.

#RESTART
vol:
VOLUME
Calculate the volume of the simulation box. More details

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
=1-192:3
SIGMA
the width to use for the gaussian kernels
=0.050
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
=env1c.pdb
REFERENCE_2
PDB files with relative distances from central atom
=env2c.pdb
MORE_THAN
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=0.5 NN=8 MM=16}
MEAN
calculate the mean of all the quantities
... ENVIRONMENTSIMILARITY
# Construct a bias potential
energy:
ENERGY
Calculate the total potential energy of the simulation box. More details

# Construct bias potential with OPES
ecv:
ECV_MULTITHERMAL_MULTIBARIC
Expand a simulation to sample multiple temperatures and pressures. More details
...
ARG
the labels of the potential energy and of the volume of the system
=energy,vol
TEMP
temperature
=330
TEMP_MIN
the minimum of the temperature range
=300
TEMP_MAX
the maximum of the temperature range
=350
PRESSURE
pressure
=0.06022140857
PRESSURE_MIN
the minimum of the pressure range
=0.06022140857
PRESSURE_MAX
the maximum of the pressure range
=0.06022140857 ...
ecv2:
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
CV_MIN
the minimum of the CV range to be explored
=0.0
CV_MAX
the maximum of the CV range to be explored
=64.0
SIGMA
sigma of the umbrella Gaussians
=1.0
BARRIER
a guess of the free energy barrier to be overcome (better to stay higher than lower)
=150
TEMP
temperature
=330
opes:
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
=ecv.*,ecv2
FILE
a file with the estimate of the relative Delta F for each component of the target and of the global c(t)
=DeltaF.data
PACE
how often the bias is updated
=100
WALKERS_MPI
switch on MPI version of multiple walkers

Q6
Calculate sixth order Steinhardt parameters. More details
SPECIES
this keyword is used for colvars such as coordination number
=1-192:3
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=0.3 D_MAX=0.35}
VMEAN
calculate the norm of the mean vector
LABEL
a label for the action so that its output can be referenced in the input to other actions
=q6
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