Project ID: plumID:19.061
Source: diffusion_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 guest molecule in the simulation guest:
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
ATOMS
the numerical indexes for the set of atoms in the group
=169-186 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
=guest
#Define the cage centre of mass centre_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
#Define the centres of the windows as the centre of the three phenyl H atoms in the window circle1:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=22,78,134 circle2:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=36,64,162 circle3:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=8,106,148 circle4:
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=50,92,120
#Define distances between the guest centre of mass and the centres of the windows of interest d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=guest_com,circle1 d2:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=guest_com,circle2
#Define distances that will need energetic walls - these are the distances to the other two windows and the overall distance from the cage centre of mass d3:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=guest_com,circle3 d4:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=guest_com,circle4 dc:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=centre_com,guest_com
lwalls:
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
=d3,d4
AT
the positions of the wall
=0.25,0.25
KAPPA
the force constant for the wall
=4500,4500
OFFSET
the offset for the start of the wall
=0,0
EXP
the powers for the walls
=2,2
EPS
the values for s_i in the expression for a wall
=1,1 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
=dc
AT
the positions of the wall
=0.45
KAPPA
the force constant for the wall
=3500
OFFSET
the offset for the start of the wall
=0
EXP
the powers for the walls
=2
EPS
the values for s_i in the expression for a wall
=1
#Deposit Gaussians, with the distances d1 and d2 as the collective variable 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,d2
SIGMA
the widths of the Gaussian hills
=0.01,0.01
HEIGHT
the heights of the Gaussian hills
=1.2
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
PACE
the frequency for hill addition
=500
GRID_MIN
the lower bounds for the grid
=-2.0,-2.0
GRID_MAX
the upper bounds for the grid
=6.0,6.0
GRID_BIN
the number of bins for the grid
=4000,4000
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,d2,d3,d4,meta.*,uwall.*,lwalls
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