PLUMED-NEST

Project ID: plumID:22.003
Source: mueller/opes/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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 
UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units

p: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
The POSITION action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the atom position
p.y
the y-component of the atom position
p.z
the z-component of the atom positionmueller: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=p.x,p.y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO ...
  
FUNC
the function you wish to evaluate
=0.15*(-200*exp(-(x-1)^2-10*y^2)-100*exp(-x^2-10*(y-0.5)^2)-170*exp(-6.5*(0.5+x)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(1+x)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2)+146.7
...
potential: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mueller
The BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Description  
potential.bias
the instantaneous value of the bias potential
potential._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filelwall: 
LOWER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.x 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=-1.3
uwall: 
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=p.x 
KAPPA
the force constant for the wall
=1000 
AT
the positions of the wall
=+1.0

opes: 
OPES_METAD
On-the-fly probability enhanced sampling with metadynamics-like target distribution. More details
 ...
  
ARG
the input for this action is the scalar output from one or more other actions
=p.x
  
PACE
the frequency for kernel deposition
=500
  
BARRIER
the free energy barrier to be overcome
=20
...

The OPES_METAD action with label opes calculates the following quantities:
 Quantity   
 Description  
opes.bias
the instantaneous value of the bias potential
opes.rct
estimate of c(t)
opes.zed
estimate of Z_n
opes.neff
effective sample size
opes.nker
total number of compressed kernels used to represent the bias
PRINT
Print quantities to a file. More details
 
FMT
the format that should be used to output real numbers
=%g 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y,mueller,opes

ENDPLUMED
Terminate plumed input. More details


run with:
mkdir $i
../../queue_md.i.sh $i

or
../loop_all.sh