PLUMED-NEST

Project ID: plumID:20.002
Source: plumed-MetaD.dat
Originally used with PLUMED version: 2.4
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. 
RESTART
Activate restart. More details
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
=npt.pdb
protein: 
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
=1-6518
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
=protein
p1: 
PATHMSD
This Colvar calculates path collective variables. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=frameset_CA.pdb 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=193.6

#metad: METAD ARG=p1.sss SIGMA=500 SIGMA_MIN=0.005 SIGMA_MAX=0.05 HEIGHT=4.184 ADAPTIVE=DIFF TEMP=300.0 BIASFACTOR=10 PACE=100
The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.sss
the position on the path
p1.zzz
the distance from the pathmetad: 
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
=p1.sss,p1.zzz 
SIGMA
the widths of the Gaussian hills
=0.2,0.02 
HEIGHT
the heights of the Gaussian hills
=0.4184 
GRID_SPARSE
 use a sparse grid to store hills
 
GRID_MIN
the lower bounds for the grid
=0,0 
GRID_MAX
the upper bounds for the grid
=40,18 
GRID_BIN
the number of bins for the grid
=200,200 
FILE
 a file in which the list of added hills is stored
=HILLS 
PACE
the frequency for hill addition
=500 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the 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
=p1.zzz 
AT
the positions of the wall
=0.16 
KAPPA
the force constant for the wall
=100000.0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall

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
=100 
FILE
the name of the file on which to output these quantities
=colvar_metaD