PLUMED-NEST

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

The UNITS action with label  calculates somethingpThe POSITION action with label p calculates the following quantities:
 Quantity   
 Type   
 Description  
p.x
scalar
the x-component of the atom position
p.y
scalar
the y-component of the atom position
p.z
scalar
the z-component of the atom position: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=1
muellerThe CUSTOM action with label mueller calculates the following quantities:
 Quantity   
 Type   
 Description  
mueller
scalar
an arbitrary function: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the values 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
...
potentialThe BIASVALUE action with label potential calculates the following quantities:
 Quantity   
 Type   
 Description  
potential.bias
scalar
the instantaneous value of the bias potential
potential.mueller_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named mueller: 
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the labels of the scalar/vector arguments whose values will be used as a bias on the system
=mueller
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
metad.rbias
scalar
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].This component can be used to obtain a reweighted histogram.
metad.rct
scalar
the reweighting factor c(t).
metad.maxbias
scalar
the maximum of the metadynamics V(s, t): 
METAD
Used to performed metadynamics on one or more collective variables. This action has hidden defaults. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=p.x
  
PACE
the frequency for hill addition
=500
  
HEIGHT
the heights of the Gaussian hills
=1
  
SIGMA
the widths of the Gaussian hills
=0.1
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
  
GRID_MIN
the lower bounds for the grid
=-2
  
GRID_MAX
the upper bounds for the grid
=2
  
GRID_BIN
the number of bins for the grid
=200
  
CALC_MAX_BIAS
 Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
metad: 
METAD
Used to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details
 ...
  
ARG
the labels of the scalars on which the bias will act
=p.x
  
PACE
the frequency for hill addition
=500
  
HEIGHT
the heights of the Gaussian hills
=1
  
SIGMA
the widths of the Gaussian hills
=0.1
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20
  
GRID_MIN
the lower bounds for the grid
=-2
  
GRID_MAX
the upper bounds for the grid
=2
  
GRID_BIN
the number of bins for the grid
=200
  
CALC_MAX_BIAS
 Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
 
FILE
 a file in which the list of added hills is stored
=HILLS
...

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 labels of the values that you would like to print to the file
=p.x,p.y,mueller,metad

ENDPLUMED
Terminate plumed input. More details


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

or
../loop_all.sh