Project ID: plumID:21.036
Source: DHH1N_sampling/BEMD/CV3/plumed.2.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


h1: 
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
=11,22,41,55,69,83,103,117,131,145,159,173,184,198,212,224,243,255,279,291,315,337,351,361,380,393,427,449,471,483,497,535,552,566,578,590,606,625,639,653,675,682

o1: 
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
=20,39,53,67,81,101,115,129,143,157,171,182,196,210,222,241,253,277,289,313,335,349,359,378,392,411,447,469,481,495,519,550,564,576,588,604,623,637,651,673,680,694

cv3: 
COORDINATION
Calculate coordination numbers. More details
 
GROUPA
First list of atoms
=h1 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=o1 
R_0
The r_0 parameter of the switching function
=0.20 
NN
 The n parameter of the switching function 
=8 
MM
 The m parameter of the switching function; 0 implies 2*NN
=10 
PAIR
 Pair only 1st element of the 1st group with 1st element in the second, etc
 
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
=3.0 
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
=cv3 
AT
the positions of the wall
=25.0 
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
=cv3 
AT
the positions of the wall
=12.0 
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
=cv3 
PACE
the frequency for hill addition
=2500 
HEIGHT
the heights of the Gaussian hills
=0.3 
SIGMA
the widths of the Gaussian hills
=0.5 
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
=46.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.1

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
=cv3,metad.bias,uwall.bias,lwall.bias
#PRINT STRIDE=10 FILE=COLVAR ARG=cv3,metad.bias