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metadynminer  

Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'
View on CRAN: Click here


Download and install metadynminer package within the R console
Install from CRAN:
install.packages("metadynminer")

Install from Github:
library("remotes")
install_github("cran/metadynminer")

Install by package version:
library("remotes")
install_version("metadynminer", "0.1.7")



Attach the package and use:
library("metadynminer")
Maintained by
Vojtech Spiwok
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-09-20
Latest Update: 2022-04-14
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.
How to cite:
Vojtech Spiwok (2018). metadynminer: Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'. R package version 0.1.7, https://cran.r-project.org/web/packages/metadynminer. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.1.2 (2018-09-20 20:20), 0.1.3 (2018-11-05 21:00), 0.1.4 (2019-03-13 08:40), 0.1.5 (2019-07-18 08:35), 0.1.6 (2019-08-20 12:50)
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