PLUMED-NEST

Project ID: plumID:19.052
Source: plumed.dat
Originally used with PLUMED version: not specified
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

UNITS
This command sets the internal units for the code. More details
 
NATURAL
 use natural units
 
# Record the volume of the simulation cell.
cell: 
CELL
Calculate the components of the simulation cell More details
# We first compute the local order parameter for each atom using the cubic harmonic function “FCCUBIC”. The sigmoid switching function “SMAP” is used to transform these quantities with a non-linear mapping on. 
# We compute the sum of these transformed order parameters using the keyword “MORE THAN”. The value of “cub.morethan” is thus proportional to the number of atoms in the fcc crystal.
# The system contains a total of 23328 real atoms, The first atom is a “ghost” atom that stays stationary at the center of the supercell. This ghost atom is only used as a reference point
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 matrixcub: 
FCCUBIC
Measure how similar the environment around atoms is to that found in a FCC structure. More details
 
SPECIES
this keyword is used for colvars such as coordination number
=2-23329 
SWITCH
the switching function that it used in the construction of the contact matrix
={CUBIC D_0=1.2 D_MAX=1.5} 
ALPHA
 The alpha parameter of the angular function that is used for FCCUBIC
=27 
MEAN
 calculate the mean of all the quantities
 
MORE_THAN1
calculate the number of variables that are more than a certain target value
={SMAP R_0=0.45 D_0=0.0 A=8 B=8}

# Perform a metadynamics simulation
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
=cub.morethan-1
PACE
the frequency for hill addition
=1000 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=600 
FILE
 a file in which the list of added hills is stored
=HILLS 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=0.58 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=400
ADAPTIVE
use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme
=DIFF 
SIGMA_MAX
the upper bounds for the sigmas (in CV units) when using adaptive hills
=300 
SIGMA_MIN
the lower bounds for the sigmas (in CV units) when using adaptive hills
=0.1 
... 

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potentialfixmax: 
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
=cub.morethan-1 
AT
the positions of the wall
=2500 
KAPPA
the force constant for the wall
=0.1
# monitor the two variables and the metadynamics bias potential 
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
ARG
the input for this action is the scalar output from one or more other actions
=cell.ax,cub.*,metad.bias,fixmax.bias 
FILE
the name of the file on which to output these quantities
=COLVAR
ENDPLUMED
Terminate plumed input. More details