PLUMED-NEST

Project ID: plumID:21.021
Source: atlas_inputs/LJ-38/plumed_biased.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} 

n4: 
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-4)*(x-4)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n5: 
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-5)*(x-5)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n6: 
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
n7: 
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-7)*(x-7)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n8: 
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
n9: 
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-9)*(x-9)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n10: 
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-10)*(x-10)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
n11: 
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-11)*(x-11)/(2*0.5*0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO


at: 
ATLAS
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=n4,n5,n6,n7,n8,n9,n10,n11 REFERENCE=cluster_plumed.dat PACE=200 SIGMA=0.1 BIASFACTOR=5 HEIGHT=0.02  GRID_MAX=5.0 GRID_BIN=500 TEMP=0.12 TRUNCATE_GRIDS ADAPTIVE_WALL=1.0 STATIC_WALL=0.0 REGULARISE=1E-12

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=n4,n5,n6,n7,n8,n9,n10,n11 
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
=200
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=at_adaptive_wall 
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
=wall 
STRIDE
 the frequency with which the quantities of interest should be output
=200
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=at 
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
=bias 
STRIDE
 the frequency with which the quantities of interest should be output
=200