Project ID: plumID:21.031
Source: plumed.dat
Originally used with PLUMED version: 2.6
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
tested onv2.9
tested onmaster
#RESTART

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=ps 
ENERGY
the units of energy
=kcal/mol

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
=1-25214
nbd1: 
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
=10888-11839,12285-14568 
nbd2: 
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
=21322-24882 
d: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=nbd1,nbd2 
NOPBC
 ignore the periodic boundary conditions when calculating distances


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
=60.0 
KAPPA
the force constant for the wall
=300.0 
EXP
 the powers for the walls
=2.0 
EPS
 the values for s_i in the expression for a wall
=1.0 
OFFSET
 the offset for the start of the wall
=0

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
=25.0 
KAPPA
the force constant for the wall
=300.0 
EXP
 the powers for the walls
=2.0 
EPS
 the values for s_i in the expression for a wall
=1.0 
OFFSET
 the offset for the start of the wall
=0

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
=d 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.0 
SIGMA
the widths of the Gaussian hills
=0.5 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=310.0
   
GRID_MIN
the lower bounds for the grid
=24.0 
GRID_MAX
the upper bounds for the grid
=61.0 
GRID_BIN
the number of bins for the grid
=150
... METAD
# monitor the variable 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
=100 
ARG
the input for this action is the scalar output from one or more other actions
=d,metad.bias 
FILE
the name of the file on which to output these quantities
=COLVAR