metadynminer3d: Tools to Read, Analyze and Visualize Metadynamics 3D 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. As an addendum, 'metadynaminer3d' is used to visualize 3D hills. 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. Free energy surfaces and minima can be plotted to produce publication quality images.

Version:	0.0.2
Depends:	R (≥ 3.3.0), metadynminer, rgl
Imports:	Rcpp, misc3d
LinkingTo:	Rcpp
Suggests:	testthat
Published:	2022-04-14
Author:	Vojtech Spiwok [aut, cre]
Maintainer:	Vojtech Spiwok <spiwokv at vscht.cz>
License:	GPL-3
URL:	https://metadynamics.cz/metadynminer3d/
NeedsCompilation:	yes
Materials:	README
CRAN checks:	metadynminer3d results

Documentation:

Reference manual:

metadynminer3d.pdf

Downloads:

Package source:	metadynminer3d_0.0.2.tar.gz
Windows binaries:	r-devel: metadynminer3d_0.0.2.zip, r-release: metadynminer3d_0.0.2.zip, r-oldrel: metadynminer3d_0.0.2.zip
macOS binaries:	r-release (arm64): metadynminer3d_0.0.2.tgz, r-oldrel (arm64): metadynminer3d_0.0.2.tgz, r-release (x86_64): metadynminer3d_0.0.2.tgz, r-oldrel (x86_64): metadynminer3d_0.0.2.tgz
Old sources:	metadynminer3d archive

Linking:

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