PLUMED-NEST

Project ID: plumID:24.004
Source: iron/plumed.start.dat
Originally used with PLUMED version: 2.8.1
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

LOAD
Loads a library, possibly defining new actions. More details
 
FILE
file to be loaded
=Graph.cpp

# Define groups for the CV
The LOAD action with label  calculates somethingC: 
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
=1-285
 
# Define the CV
The GROUP action with label C calculates something
GRAPH
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
 LABEL=model
 ATOMS=C
 KCUT=50
 MODEL=model.pt
... GRAPH

METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
 
ARG
the input for this action is the scalar output from one or more other actions
=model.node-0,model.node-1
 
SIGMA
the widths of the Gaussian hills
=0.6,0.6 
 
HEIGHT
the heights of the Gaussian hills
=15 # this is 0.5kt at 1800 K 
 
FILE
 a file in which the list of added hills is stored
=HILLS   # File where the information of the gaussians is printed
 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=50
 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=1800.0 
 
PACE
the frequency for hill addition
=500
 
GRID_MIN
the lower bounds for the grid
=1.0,1.0 
GRID_MAX
the upper bounds for the grid
=15.0,15.0
 
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD

The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=model.*,metad 
STRIDE
 the frequency with which the quantities of interest should be output
=500 
FILE
the name of the file on which to output these quantities
=COLVAR