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
The RESTART action with label  calculates something
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
proteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
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
=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
p1The PATHMSD action with label p1 calculates the following quantities:
 Quantity   
 Type   
 Description  
p1.sss
scalar
the position on the path
p1.zzz
scalar
the distance from the path: 
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
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
=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
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
=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 labels of the values that you would like to print to the file
 
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