PLUMED-NEST

Project ID: plumID:21.036
Source: DHH1N_sampling/PTMetaD-WTE/plumed_PE_PTMetaD-WTE.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

eneThe ENERGY action with label ene calculates the following quantities:
 Quantity   
 Type   
 Description  
ene
scalar
the internal energy: 
ENERGY
Calculate the total potential energy of the simulation box. More details
enedThe METAD action with label ened calculates the following quantities:
 Quantity   
 Type   
 Description  
ened.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
=ene 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=1.2 
SIGMA
the widths of the Gaussian hills
=2000.0 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=12 
FILE
 a file in which the list of added hills is stored
=HILLS
PRINT
Print quantities to a file. More details
 
STRIDE
 the frequency with which the quantities of interest should be output
=5000 
ARG
the labels of the values that you would like to print to the file
=ene,ened.bias 
FILE
the name of the file on which to output these quantities
=COLVAR_ENE