PLUMED-NEST

Project ID: plumID:19.047
Source: trpcage/normal/plumed.dat
Originally used with PLUMED version: 2.5
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
=1-304
p1: 
PROPERTYMAP
Calculate generic property maps. More details
 
REFERENCE
the pdb is needed to provide the various milestones
=reframe.pdb 
PROPERTY
the property to be used in the indexing: this goes in the REMARK field of the reference
=X,Y 
LAMBDA
the lambda parameter is needed for smoothing, is in the units of plumed
=50.0 
NEIGH_SIZE
size of the neighbor list
=50 
NEIGH_STRIDE
how often the neighbor list needs to be calculated in time units
=50
The PROPERTYMAP action with label p1 calculates the following quantities:
 Quantity   
 Description  
p1.zzz
the label of this action is set by user in the input
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.X,p1.Y 
SIGMA
the widths of the Gaussian hills
=0.1,0.1 
HEIGHT
the heights of the Gaussian hills
=0.5 
PACE
the frequency for hill addition
=500 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=restraint
The METAD action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the 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
=p1.X,p1.Y,p1.zzz,restraint.bias 
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 
FMT
the format that should be used to output real numbers
=%8.4f