metadynminer

Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'

Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) <doi:10.1016/j.cpc.2013.09.018> program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) <doi:10.1016/j.cpc.2015.08.037> to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) <doi:10.1063/1.1323224>. Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.

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Description file content

Package
metadynminer
Type
Package
Title
Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
Version
0.1.3
Date
2018-11-05
Depends
R (>= 3.3.0)
LinkingTo
Rcpp
Description
Metadynamics is a state of the art biomolecular simulation technique. 'Plumed' Tribello, G.A. et al. (2014) program makes it possible to perform metadynamics using various simulation codes. The results of metadynamics done in 'Plumed' can be analyzed by 'metadynminer'. The package 'metadynminer' reads 1D and 2D metadynamics hills files from 'Plumed' package. It uses a fast algorithm by Hosek, P. and Spiwok, V. (2016) to calculate a free energy surface from hills. Minima can be located and plotted on the free energy surface. Transition states can be analyzed by Nudged Elastic Band method by Henkelman, G. and Jonsson, H. (2000) . Free energy surfaces, minima and transition paths can be plotted to produce publication quality images.
LazyData
true
License
GPL-3
RoxygenNote
6.1.0
Imports
Rcpp
URL
NeedsCompilation
yes
Packaged
2018-11-05 19:25:59 UTC; spiwokv
Author
Vojtech Spiwok [aut, cre] ()
Maintainer
Vojtech Spiwok
Repository
CRAN
Date/Publication
2018-11-05 20:00:02 UTC

install.packages('metadynminer')

0.1.3

12 days ago

http://www.metadynamics.cz/metadynminer

Vojtech Spiwok

GPL-3

Depends on

R (>= 3.3.0)

Imports

Rcpp

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