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.

Version: 0.1.2
Depends: R (≥ 3.3.0)
Imports: Rcpp
LinkingTo: Rcpp
Published: 2018-09-20
Author: Vojtech Spiwok ORCID iD [aut, cre]
Maintainer: Vojtech Spiwok <spiwokv at vscht.cz>
License: GPL-3
URL: http://www.metadynamics.cz/metadynminer
NeedsCompilation: yes
Materials: README
CRAN checks: metadynminer results

Downloads:

Reference manual: metadynminer.pdf
Package source: metadynminer_0.1.2.tar.gz
Windows binaries: r-devel: metadynminer_0.1.2.zip, r-release: metadynminer_0.1.2.zip, r-oldrel: metadynminer_0.1.2.zip
OS X binaries: r-release: metadynminer_0.1.2.tgz, r-oldrel: metadynminer_0.1.2.tgz

Linking:

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