PLUMED-NEST

Project ID: plumID:23.015
Source: OPEX_and_METAD/github_opex_100d/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
=1-277 
ENTITY1
the atoms that make up a molecule that you wish to align
=278-554

c1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-25
c2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=278-302

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
=555-40457:3
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 
=12 
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 
=12 
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: 
OPES_METAD_EXPLORE
On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. More details
 ...
   
ARG
the input for this action is the scalar output from one or more other actions
=d,cna
   
PACE
the frequency for kernel deposition
=500
   
BARRIER
the free energy barrier to be overcome
=50
   
FILE
 a file in which the list of all deposited kernels is stored
=kernals.data
   
WALKERS_MPI
 switch on MPI version of multiple walkers
   
NLIST
 use neighbor list for kernels summation, faster but experimental
...

The OPES_METAD_EXPLORE action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rct
estimate of c(t)
metad.zed
estimate of Z_n
metad.neff
effective sample size
metad.nker
total number of compressed kernels used to represent the bias
metad.nlker
number of kernels in the neighbor list
metad.nlsteps
number of steps from last neighbor list updateuwall: 
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
 
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.data 
ARG
the input for this action is the scalar output from one or more other actions