Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV5/plumed.4.dat
Originally used with PLUMED version: 2.5.2
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
STRUCTURE
a file in pdb format containing a reference structure
=Protein.pdb
MOLTYPE
what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
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
=1-709
RANDOM_EXCHANGES
Set random pattern for exchanges. More details

cv5:
ALPHARMSD
Probe the alpha helical content of a protein structure. More details
RESIDUES
this command is used to specify the set of residues that could conceivably form part of the secondary structure
=1-45
TYPE
the manner in which RMSD alignment is performed
=DRMSD
R_0
The r_0 parameter of the switching function
=0.08
NN
The n parameter of the switching function
=2
MM
The m parameter of the switching function
=4
NOPBC
ignore the periodic boundary conditions

lwall:
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
=cv5
AT
the positions of the wall
=2.0
KAPPA
the force constant for the wall
=30.0 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
=cv5
AT
the positions of the wall
=15.0
KAPPA
the force constant for the wall
=30.0
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
=cv5
PACE
the frequency for hill addition
=2500
HEIGHT
the heights of the Gaussian hills
=0.3
SIGMA
the widths of the Gaussian hills
=0.1
FILE
a file in which the list of added hills is stored
=HILLS
GRID_MIN
the lower bounds for the grid
=0.0
GRID_MAX
the upper bounds for the grid
=30.0
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.025
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
=cv5,metad.bias,uwall.bias,lwall.bias
FILE
the name of the file on which to output these quantities
=COLVAR #PRINT STRIDE=10 ARG=cv5,metad.bias FILE=COLVAR