Project ID: plumID:23.034
Source: SS_model/plumed.dat
Originally used with PLUMED version: 2.7.2
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 onv2.10
tested onmaster
tested on master
# Restart simulation. This command will append results of new simulations to the same output files, e.g. COLVAR.
# RESTART

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=PairOrientationalEntropy.cpp

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=ManyAnglePlus.cpp

# Define groups for the CV

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=centers.dat
C: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-2400:8
O: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=2-2400:8
N1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=3-2400:8
N2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=6-2400:8
 
# Define the CV

PAIR_ORIENTATIONAL_ENTROPY
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 LABEL=s1
 CENTER=C
 START=Ncenter
 END=O
 MAXR=0.6
 SIGMA=0.05,0.25
... PAIR_ORIENTATIONAL_ENTROPY

PAIR_ORIENTATIONAL_ENTROPY
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 LABEL=s2
 CENTER=C
 START=N1
 END=N2
 MAXR=0.6
 SIGMA=0.05,0.125
 UP_DOWN_SYMMETRY
... PAIR_ORIENTATIONAL_ENTROPY

MANY_ANGLE_PLUS
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 LABEL=ma1
 CENTER=C
 START=Ncenter
 END=O
 RCUT=1.0
 NOPBC
 MEAN
 MOMENT2
... MANY_ANGLE_PLUS

MANY_ANGLE_PLUS
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 LABEL=ma2
 CENTER=C
 START=N1
 END=N2
 RCUT=1.0
 NOPBC
 MEAN
 MOMENT2
... MANY_ANGLE_PLUS

COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of This action is a shortcut. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cn 
SPECIES
this keyword is used for colvars such as coordination number
=Ncenter
 
SWITCH
the switching function that it used in the construction of the contact matrix
={RATIONAL R_0=0.6 D_MAX=0.8}
 
MORE_THAN1
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=8.0 D_MAX=9.0}
 
MORE_THAN2
calculate the number of variables that are more than a certain target value
={RATIONAL R_0=11.0 D_MAX=12.0}
 
MOMENTS
the list of moments that you would like to calculate
=2
 
LOWMEM
 this flag does nothing and is present only to ensure back-compatibility

... COORDINATIONNUMBER

# Construct a bias potential using metadynamics

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=s1,s2   # Label of the CV
 
PACE
the frequency for hill addition
=500   # Pace in the deposition of the gaussians
 
HEIGHT
the heights of the Gaussian hills
=5.0   # Height of the gaussians in energy units kJ/mol. This is around 2 kT. 1kT = 2.494339
 
SIGMA
the widths of the Gaussian hills
=0.2,0.2   # Width of the gaussian in CV units
 
FILE
 a file in which the list of added hills is stored
=HILLS   # File where the information of the gaussians is printed
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=100.0   # Bias factor in well tempered simulations
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0   # Temperature in Kelvin. Only needed for well tempered simulations
 
GRID_MIN
the lower bounds for the grid
=-15.0,-15.0   # The following three lines define a grid for the calculation of the bias potential. Use it **always**.
 
GRID_MAX
the upper bounds for the grid
=0.0,0.0
 
GRID_BIN
the number of bins for the grid
=600,600
 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]

... METAD

# Print value of the CV and bias to a file named COLVAR

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