PLUMED-NEST

Project ID: plumID:19.023
Source: plumed.dat
Originally used with PLUMED version: 2.3
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

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
=1,5,6,7,9,11,15,16,17,19
#variables
The WHOLEMOLECULES action with label  calculates somethingphiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=5,7,9,15
psiThe TORSION action with label psi calculates the following quantities:
 Quantity   
 Type   
 Description  
psi
scalar
the TORSION involving these atoms: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=7,9,15,17
rgThe GYRATION action with label rg calculates the following quantities:
 Quantity   
 Type   
 Description  
rg
scalar
the 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
=1,5,6,7,9,11,15,16,17,19
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=phi,psi,rg 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=100
#Well-tempered MetaD lines, one for each CV. For each replica the value of the BIASFACTOR should be changed.
aThe METAD action with label a calculates the following quantities:
 Quantity   
 Type   
 Description  
a.bias
scalar
the instantaneous value of the bias potential: 
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
=phi 
SIGMA
the widths of the Gaussian hills
=0.3 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=12 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
FILE
 a file in which the list of added hills is stored
=HILLSphi
bThe METAD action with label b calculates the following quantities:
 Quantity   
 Type   
 Description  
b.bias
scalar
the instantaneous value of the bias potential: 
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
=psi 
SIGMA
the widths of the Gaussian hills
=0.3 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=12 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=-pi 
GRID_MAX
the upper bounds for the grid
=pi 
FILE
 a file in which the list of added hills is stored
=HILLSpsi
cThe METAD action with label c calculates the following quantities:
 Quantity   
 Type   
 Description  
c.bias
scalar
the instantaneous value of the bias potential: 
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
=rg 
SIGMA
the widths of the Gaussian hills
=0.007 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=12 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=0.4 
FILE
 a file in which the list of added hills is stored
=HILLSrg