PLUMED-NEST

Project ID: plumID:21.021
Source: meta_inputs/LJ-38/plumed.dat
Originally used with PLUMED version: 2.7-mod
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

#
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
nsa: 
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
 
SPECIES
this keyword is used for colvars such as coordination number
=1-38 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.25 D_MAX=1.5} #MORE_THAN={GAUSSIAN R_0=0.5 D_0=6}

ns: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=nsa 
FUNC
the function you wish to evaluate
=exp(-(x-6)*(x-6)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
ne: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=nsa 
FUNC
the function you wish to evaluate
=exp(-(x-8)*(x-8)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

mt: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=ns,ne 
PACE
the frequency for hill addition
=500 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
HEIGHT
the heights of the Gaussian hills
=1.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=0.12 
GRID_MIN
the lower bounds for the grid
=0.,0 
GRID_MAX
the upper bounds for the grid
=28,20 
GRID_BIN
the number of bins for the grid
=300,300
...

The METAD action with label mt calculates the following quantities:
 Quantity   
 Description  
mt.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ns,ne,mt.bias 
FMT
the format that should be used to output real numbers
=%8.4f 
FILE
the name of the file on which to output these quantities
=colvar 
STRIDE
 the frequency with which the quantities of interest should be output
=500