PLUMED-NEST

Project ID: plumID:21.041
Source: plumed.dat
Originally used with PLUMED version: 2.5
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

# PLUMED works internally in kJ/nm/ps if no UNITS command is used in PLUMED input file
u_cn:     
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=1-256 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=257-512 
NN
 The n parameter of the switching function 
=6 
MM
 The m parameter of the switching function; 0 implies 2*NN
=12 
D_0
 The d_0 parameter of the switching function
=0.13 
R_0
The r_0 parameter of the switching function
=0.21 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=0.8 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5000
The COORDINATION action with label u_cn calculates a scalar quantityu_vol:    
VOLUME
Calculate the volume of the simulation box. More details

## Two different ions groups are distinguished by their ID e.g (1-256) for Na+ ions and (257 - 512) for Cl- ions

The VOLUME action with label u_vol calculates a scalar quantitycn:       
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=u_cn     
COEFFICIENTS
 the coefficients of the arguments in your function
=0.003906250000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Number 0.003906250000 equals to 2.0/512, where 512 stands for the system size.
# The number is the prefactor for the average coordination number (see Eq. (1) in Phys. Rev. Let. 127, 105701 (2021))

volume:   
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=u_vol    
COEFFICIENTS
 the coefficients of the arguments in your function
=1.953125000000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Number 1.953125000000 equals to 1000/512
# where 512 stands for system size and 1000 ensures the change of units from nm^3 to A^3.

scale_cn:  
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=cn      
PARAMETERS
 the parameters of the arguments in your function
=7.822   
COEFFICIENTS
 the coefficients of the arguments in your function
=0.12784454103809767  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
scale_vol: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=volume  
PARAMETERS
 the parameters of the arguments in your function
=13.089  
COEFFICIENTS
 the coefficients of the arguments in your function
=0.07640003056001222 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# 0.127... is the inverse value of 7.822, the mean coordination number in the starting phase
# 0.076... is the inverse value of 13.089, the mean volume in the starting phase (in A^3)

easy:      
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=scale_vol,scale_cn  
FUNC
the function you wish to evaluate
=((-0.8151947133609164)*x+(0.5791869985664506)*y  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
difficult: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input to this function
=scale_vol,scale_cn  
FUNC
the function you wish to evaluate
=((0.5791869985664506)*x+(0.8151947133609164)*y  
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Values above are coefficients obtained by diagonalisation of covariance matrix
# see Supplemental Material of Phys. Rev. Let. 127, 105701 (2021)

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
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=easy,difficult
 
SIGMA
the widths of the Gaussian hills
=0.002,0.001
 
HEIGHT
the heights of the Gaussian hills
=3.0
 
PACE
the frequency for hill addition
=500
 
GRID_MIN
the lower bounds for the grid
=-1,-1
 
GRID_MAX
the upper bounds for the grid
=1,1
 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.001,0.001
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
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
=10

ENDPLUMED
Terminate plumed input. More details