PLUMED-NEST

Project ID: plumID:21.023
Source: Data-mb/mb-wtm-bf7/plumed.dat
Originally used with PLUMED version: 2.7
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

INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=./MuellerBrown-Potential.dat
# The command:
# INCLUDE FILE=./MuellerBrown-Potential.dat
# ensures PLUMED loads the contents of the file called ./MuellerBrown-Potential.dat
# The contents of this file are shown below (click the red comment to hide them).
# 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

# Müller-Brown potential, sum of four terms
#-200*exp( -(x-1)^2 -10*y^2 )
#-100*exp( -x^2 -10*(y-0.5)^2 )
#-170*exp( -6.5*(x+0.5)^2 + 11*(x+0.5)*(y-1.5) -6.5*(y-1.5)^2 )
# +15*exp(  0.7*(x+1)^2 +0.6*(x+1)*(y-1) +0.7*(y-1)^2 )
# Shifted by 146.699489200588 to have a zero value 
# at the global minimum ( -0.558 , 1.442 )
# Minima: ( -0.558 , 1.442 ) [ Value: 0.0 ]
#         (  0.623 , 0.028 ) [ Value: 38.532839 ]
#         ( -0.050 , 0.467 ) [ Value: 65.931740 ] 
# Saddle Points : ( -0.822 ,  0.624 ) [ Value: 106.034644 ]
#                 ( -0.212 ,  0.293 ) [ Value: 88.435607 ]
# Can be scaled via the scaling_factor 
# (above values for minima and saddle points are then scaled)

scaling_factor: 
CONSTANT
Create a constant value that can be passed to actions More details
 
VALUE
the single number that you would like to store
=0.2

The CONSTANT action with label scaling_factor calculates a scalar quantityp: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1,2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label p calculates the following quantities:
 Quantity   
 Description  
p.x
the x-component of the vector connecting the two atoms
p.y
the y-component of the vector connecting the two atoms
p.z
the z-component of the vector connecting the two atoms
CUSTOM
Calculate a combination of variables using a custom expression. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=pot
 
ARG
the input to this function
=p.x,p.y,scaling_factor 
 
VAR
the names to give each of the arguments in the function
=x,y,sf
 
FUNC
the function you wish to evaluate
=sf*(-200*exp(-(x-1)^2-10*y^2)-100*exp(-x^2-10*(y-0.5)^2)-170*exp(-6.5*(x+0.5)^2+11*(x+0.5)*(y-1.5)-6.5*(y-1.5)^2)+15*exp(0.7*(x+1)^2+0.6*(x+1)*(y-1)+0.7*(y-1)^2)+146.699489200588
 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
... CUSTOM
bv: 
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
=pot
# --- End of included input --- 
The BIASVALUE action with label bv calculates the following quantities:
 Quantity   
 Description  
bv.bias
the instantaneous value of the bias potential
bv._bias
one or multiple instances of this quantity can be referenced elsewhere in the input file
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
=mtd

  
ARG
the input for this action is the scalar output from one or more other actions
=p.x,p.y
  
PACE
the frequency for hill addition
=100
  
SIGMA
the widths of the Gaussian hills
=0.1,0.1
  
HEIGHT
the heights of the Gaussian hills
=1.5

  
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1
 
  
BIASFACTOR
use well tempered metadynamics and use this bias factor
=7
  
GRID_MIN
the lower bounds for the grid
=-5,-5
  
GRID_MAX
the upper bounds for the grid
=5,5
  
GRID_BIN
the number of bins for the grid
=500,500
  
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
  
RCT_USTRIDE
the update stride for calculating the $c(t)$ reweighting factor
=1
... METAD

The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.bias
the instantaneous value of the bias potential
mtd.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
mtd.rct
the reweighting factor $c(t)$w: 
REWEIGHT_METAD
Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system. More details
 
TEMP
the system temperature
=1

The REWEIGHT_METAD action with label w calculates a scalar quantity
PRINT
Print quantities to a file. More details
 
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.data 
STRIDE
 the frequency with which the quantities of interest should be output
=200