PLUMED-NEST

Project ID: plumID:23.039
Source: fullerene/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. 
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=nvt.pdb
# bias the distance of the 'methane molecule' from the center of the box
The MOLINFO action with label  calculates somethingc1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=8121-9020 
NOPBC
 ignore the periodic boundary conditions when calculating distances
The CENTER action with label c1 calculates somethingc2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=9021-9080
The CENTER action with label c2 calculates somethingd1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=c1,c2 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.x
the x-component of the vector connecting the two atoms
d1.y
the y-component of the vector connecting the two atoms
d1.z
the z-component of the vector connecting the two atoms
d1.value
the DISTANCE between this pair of atomstmp: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=d1.x,d1.y 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The COMBINE action with label tmp calculates somethingrho: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=tmp 
POWERS
 the powers to which you are raising each of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
# since I don't see a spring constant defined in the SI of the paper,
# I will use a spring constant of 2 kT
The COMBINE action with label rho calculates somethinguwall: 
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
=d1.z 
AT
the positions of the wall
=2.1 
KAPPA
the force constant for the wall
=100000.0 
EXP
 the powers for the walls
=4
The UPPER_WALLS action with label uwall calculates somethingp: 
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the arguments on which the bias is acting
=rho 
AT
the position of the restraint
=0.0 
KAPPA
 specifies that the restraint is harmonic and what the values of the force constants on each of the variables are
=1000.0
The RESTRAINT action with label p calculates somethingmetad: 
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
=d1.z
   # Deposit a Gaussian every 300 time steps, with initial height equal to 2.0 kJ/mol
   
PACE
the frequency for hill addition
=300 
HEIGHT
the heights of the Gaussian hills
=2.0
   # the bias factor should be chosen wisely
   
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
   # Gaussian width (sigma) should be chosen based on CV fluctuation in unbiased run
   
SIGMA
the widths of the Gaussian hills
=0.03
   #Gaussians will be written to file and also stored on grid
   
GRID_MIN
the lower bounds for the grid
=-1 
GRID_MAX
the upper bounds for the grid
=5
   
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
...
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
DUMPMASSCHARGE
Dump masses and charges on a selected file. More details
 
FILE
file on which to output charges and masses
=mcfile
# Print both collective variables and the value of the bias potential on COLVAR file
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 
STRIDE
 the frequency with which the quantities of interest should be output
=100