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.

Getting started

Package details

AuthorVojtech Spiwok [aut, cre] (<https://orcid.org/0000-0001-8108-2033>)
MaintainerVojtech Spiwok <spiwokv@vscht.cz>
LicenseGPL-3
Version0.0.1
URL http://www.metadynamics.cz/metadynminer3d
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("metadynminer3d")

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metadynminer3d documentation built on July 28, 2019, 5:03 p.m.