PLUMED-NEST

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

#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

The MOLINFO action with label  calculates something
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

h1The GROUP action with label h1 calculates the following quantities:
 Quantity   
 Type   
 Description  
h1
atoms
indices of atoms specified in GROUP: 
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

o1The GROUP action with label o1 calculates the following quantities:
 Quantity   
 Type   
 Description  
o1
atoms
indices of atoms specified in GROUP: 
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

cv3The COORDINATION action with label cv3 calculates the following quantities:
 Quantity   
 Type   
 Description  
cv3
scalar
the value of the coordination: 
COORDINATION
Calculate coordination numbers. This action has hidden defaults. 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
cv3: 
COORDINATION
Calculate coordination numbers. This action uses the defaults shown here. 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  
D_0
 The d_0 parameter of the switching function
=0.0

uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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
lwallThe LOWER_WALLS action with label lwall calculates the following quantities:
 Quantity   
 Type   
 Description  
lwall.bias
scalar
the instantaneous value of the bias potential
lwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: 
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

metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the labels of the scalars on which the bias will act
=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 labels of the values that you would like to print to the file
=cv3,metad.bias,uwall.bias,lwall.bias
#PRINT STRIDE=10 FILE=COLVAR ARG=cv3,metad.bias