Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV2/plumed.1.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


cg: 
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
=27,31,47,61,75,89,109,124,137,151,165,190,205,218,230,249,261,285,297,321,344,367,386,399,403,421,433,455,477,490,503,529,541,559,572,584,595,599,612,631,646,659,688,703

cv2: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=cg 
R_0
The r_0 parameter of the switching function
=0.5 
NN
 The n parameter of the switching function 
=8 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
NLIST
 Use a neighbor list to speed up the calculation
 
NL_CUTOFF
The cutoff for the neighbor list
=4.0 
NL_STRIDE
The frequency with which we are updating the atoms in the neighbor list
=5

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
=cv2 
AT
the positions of the wall
=210.0 
KAPPA
the force constant for the wall
=30.0
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
=cv2 
AT
the positions of the wall
=80.0 
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
=cv2 
PACE
the frequency for hill addition
=2500 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=2.0 
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
=300.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.25

PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=10 
FILE
the name of the file on which to output these quantities
=COLVAR 
ARG
the input for this action is the scalar output from one or more other actions
=cv2,metad.bias,uwall.bias,lwall.bias
#PRINT STRIDE=10 FILE=COLVAR ARG=cv2,metad.bias