PLUMED-NEST

Project ID: plumID:19.079
Source: nest/ha_doc/plumed.dat
Originally used with PLUMED version: 2.4.2
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein 
STRUCTURE
a file in pdb format containing a reference structure
=conf.pdb

The MOLINFO action with label  calculates somethingeneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the value calculated by this action: 
ENERGY
Calculate the total potential energy of the simulation box. More details

#PEPTIDE
pep1The COM action with label pep1 calculates the following quantities:
 Quantity   
 Type   
 Description  
pep1
atoms
virtual atom calculated by COM action: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=1-250
refThe GROUP action with label ref calculates the following quantities:
 Quantity   
 Type   
 Description  
ref
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
=4900
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1.x
scalar
the x-component of the vector connecting the two atoms
d1.y
scalar
the y-component of the vector connecting the two atoms
d1.z
scalar
the z-component of the vector connecting the two atoms: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=ref,pep1 
COMPONENTS
 calculate the x, y and z components of the distance separately and store them as label
 
NOPBC
 ignore the periodic boundary conditions when calculating distances

##radius of gyration##
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=5,28,40,54,66,85,102,114,138,162,177,193,204,219,238 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the radius of gyration


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
=ene
PACE
the frequency for hill addition
=2500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0 
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=400
GRID_MIN
the lower bounds for the grid
=-1700000.0
GRID_MAX
the upper bounds for the grid
=-1400000.0
FILE
 a file in which the list of added hills is stored
=HILLS
... METAD


#MTD
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
=d1.z,rg
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0 
HEIGHT
the heights of the Gaussian hills
=2.0
SIGMA
the widths of the Gaussian hills
=0.01,0.02
GRID_MIN
the lower bounds for the grid
=0.0,0.0
GRID_MAX
the upper bounds for the grid
=10.0,10.0
FILE
 a file in which the list of added hills is stored
=HILLS_MTD
LABEL
a label for the action so that its output can be referenced in the input to other actions
=cvbiasThe METAD action with label cvbias calculates the following quantities:
 Quantity   
 Type   
 Description  
cvbias.bias
scalar
the instantaneous value of the bias potential
... METAD


## wall 
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
=d1.z 
AT
the positions of the wall
=4.5 
KAPPA
the force constant for the wall
=50000 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=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

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR