PLUMED-NEST

Project ID: plumID:23.015
Source: OPEX_and_METAD/github_metad_0d/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

WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-295 
ENTITY1
the atoms that make up a molecule that you wish to align
=296-590

c1: 
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
=1-295
c2: 
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
=296-590

d: 
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

The DISTANCE action with label d calculates a scalar quantityOW: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=591-40598:3
cn1: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=c1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=OW 
R_0
The r_0 parameter of the switching function
=1.0 
NN
 The n parameter of the switching function 
=16 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.5 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=500
The COORDINATION action with label cn1 calculates a scalar quantitycn2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=c2 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=OW 
R_0
The r_0 parameter of the switching function
=1.0 
NN
 The n parameter of the switching function 
=16 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=1.5 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=500
The COORDINATION action with label cn2 calculates a scalar quantitycna: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=cn1,cn2 
FUNC
the function you wish to evaluate
=0.5*(x+y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

metad: 
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
=d,cna
   
PACE
the frequency for hill addition
=500
   
HEIGHT
the heights of the Gaussian hills
=3 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
   
SIGMA
the widths of the Gaussian hills
=0.1,2
   
FILE
 a file in which the list of added hills is stored
=HILLS
...

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialuwall: 
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
=d 
AT
the positions of the wall
=3.5 
KAPPA
the force constant for the wall
=10000
lwall: 
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
=d 
AT
the positions of the wall
=1.2 
KAPPA
the force constant for the wall
=10000

PRINT
Print quantities to a file. More details
  
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.data 
ARG
the input for this action is the scalar output from one or more other actions