PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV6/plumed.5.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

#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

cv6: 
ANTIBETARMSD
Probe the antiparallel beta sheet content of your 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
=8 
MM
 The m parameter of the switching function
=12 
NOPBC
 ignore the periodic boundary conditions

The ANTIBETARMSD action with label cv6 calculates the following quantities:
 Quantity   
 Description  
cv6.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
cv6.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the thresholdlwall: 
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
=cv6 
AT
the positions of the wall
=0.0 
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
=cv6 
AT
the positions of the wall
=9.0 
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
=cv6 
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

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
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
=cv6,metad.bias,uwall.bias,lwall.bias 
FILE
the name of the file on which to output these quantities
=COLVAR
#PRINT STRIDE=10 ARG=cv6,metad.bias FILE=COLVAR