PLUMED-NEST

Project ID: plumID:20.019
Source: Crystal-Energy-Landscapes/plumed.dat
Originally used with PLUMED version: 2.3-mod
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

#RESTART

# Avoid too skewed triclinic box
cell: 
CELL
Calculate the components of the simulation cell More details

The CELL action with label cell calculates the following quantities:
 Quantity   
 Description  
cell.ax
the ax component of the cell matrix
cell.ay
the ay component of the cell matrix
cell.az
the az component of the cell matrix
cell.bx
the bx component of the cell matrix
cell.by
the by component of the cell matrix
cell.bz
the bz component of the cell matrix
cell.cx
the cx component of the cell matrix
cell.cy
the cy component of the cell matrix
cell.cz
the cz component of the cell matrixbx: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cell.bx,cell.ax 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cx: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cell.cx,cell.ax 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cy: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=cell.cy,cell.by 
FUNC
the function you wish to evaluate
=abs(x)-0.5*y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

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
=bx,cx,cy 
AT
the positions of the wall
=0.0,0.0,0.0 
KAPPA
the force constant for the wall
=100000.0,100000.0,100000.0 
EXP
 the powers for the walls
=2,2,2 
EPS
 the values for s_i in the expression for a wall
=1,1,1 
OFFSET
 the offset for the start of the wall
=0.3,0.3,0.3 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

# CV1 - Density
vol: 
VOLUME
Calculate the volume of the simulation box. More details
The VOLUME action with label vol calculates a scalar quantitydensity: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=vol 
FUNC
the function you wish to evaluate
=400.0/x*1.66054*118.0 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# Constraints to force the system to stay in the grid 
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
=density 
AT
the positions of the wall
=1800 
KAPPA
the force constant for the wall
=100.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=ulimit
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
=density 
AT
the positions of the wall
=1200 
KAPPA
the force constant for the wall
=100.0 
EXP
 the powers for the walls
=2 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=25 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=llimit

#CV2 - Potential Energy 
ene_pot: 
ENERGY
Calculate the total potential energy of the simulation box. More details
elatt: 
MATHEVAL
An alias to the 
ef CUSTOM function. More details
 
ARG
the input to this function
=ene_pot,uwall.bias,ulimit.bias,llimit.bias 
VAR
the names to give each of the arguments in the function
=a,b,c,d 
FUNC
the function you wish to evaluate
=(a-b-c-d)/400.0+350.507 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# WTmetaD Parameters
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
=elatt,density
PACE
the frequency for hill addition
=1000
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=2.0,20.0
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
BIASFACTOR
use well tempered metadynamics and use this bias factor
=200.0
GRID_MIN
the lower bounds for the grid
=-120,1200
GRID_MAX
the upper bounds for the grid
=400,1800
GRID_BIN
the number of bins for the grid
=5200,600
# PLUMED 2.3 syntax
# REWEIGHTING_NGRID=5200,600
# REWEIGHTING_NHILLS=10
# PLUMED 2.4 syntax
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
# RCT_USTRIDE=10
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD

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)$
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
ARG
the input for this action is the scalar output from one or more other actions
=elatt,density,metad.bias,metad.rbias,metad.rct,ulimit.bias,llimit.bias,uwall.bias 
FILE
the name of the file on which to output these quantities
=COLVAR