Project ID: plumID:19.061
Source: ple_meta.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
tested onv2.9
tested onmaster
#Restart the simulation

RESTART
Activate restart. More details


#Define the cage and guest centres of mass and the distance between them
cage_com: 
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
=1-168
guest_com: 
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
=169-186

d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=cage_com,guest_com 
NOPBC
 ignore the periodic boundary conditions when calculating distances


#Define the energetic wall for the system, to prevent the guest moving too far from the cage
uwall: 
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
=d1 
AT
the positions of the wall
=2.4 
KAPPA
the force constant for the wall
=150.0 
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
=0

#Deposit Gaussians using the distance between the centres of mass as the collective variable, and print the output to the COLVAR file
meta: 
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
=d1 
SIGMA
the widths of the Gaussian hills
=0.05 
HEIGHT
the heights of the Gaussian hills
=1.2 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
GRID_MIN
the lower bounds for the grid
=-1.0 
GRID_MAX
the upper bounds for the grid
=5.0 
GRID_BIN
the number of bins for the grid
=2400

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,meta.*,uwall 
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
=2000