Project ID: plumID:19.077
Source: 6mer_NH.dat
Originally used with PLUMED version: 2.4
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
MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
MOLTYPE
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
STRUCTURE
a file in pdb format containing a reference structure
=6mer.pdb
#PEPTIDE DISTANCE# pep1:
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
=1-104 d1:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=2383,pep1
COMPONENTS
calculate the x, y and z components of the distance separately and store them as label
NOPBC
ignore the periodic boundary conditions when calculating distances

##radius of gyration##
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
TYPE
The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5,29,51,72,84,96
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rg
##ENERGY## ene:
ENERGY
Calculate the total potential energy of the simulation box. More details

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
=ene
PACE
the frequency for hill addition
=5000
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
HEIGHT
the heights of the Gaussian hills
=2.00
SIGMA
the widths of the Gaussian hills
=280
GRID_MIN
the lower bounds for the grid
=-5500000.000000
GRID_MAX
the upper bounds for the grid
=-5000000.000000
FILE
a file in which the list of added hills is stored
=HILLS ... METAD
wall1:
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.z
AT
the positions of the wall
=4.0
KAPPA
the force constant for the wall
=1500
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.z,rg
PACE
the frequency for hill addition
=250
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15.0
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.01,0.02
GRID_MIN
the lower bounds for the grid
=0.0,0.0
GRID_MAX
the upper bounds for the grid
=20.0,10.0
FILE
a file in which the list of added hills is stored
=HILLS_MTD
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cvbias ... METAD
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.z,rg
STRIDE
the frequency with which the quantities of interest should be output
=500
FILE
the name of the file on which to output these quantities
=COLVAR