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metadynminer
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]
[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
Previous versions and publish date:
Other packages that cited metadynminer R package
View metadynminer citation profile
Other R packages that metadynminer depends,
imports, suggests or enhances
Functions, R codes and Examples using
the metadynminer R package
Some associated functions: acealanme . acealanme1d . emptyhills . feprof.minima . feprof . fes.hillsfile . fes . fes2.hillsfile . fes2 . fes2d21d . fesminima.fes . fesminima . fespoint.hillsfile . fespoint . head.hillsfile . lines.fes . lines.hillsfile . lines.nebpath . linesonfes . max.fes . min.fes . neb . oneminimum.fes . oneminimum . plot.fes . plot.hillsfile . plot.minima . plot.nebpath . plot.profiles . plotheights.hillsfile . plotheights . points.fes . points.hillsfile . points.nebpath . pointsonfes . print.fes . print.hillsfile . print.minima . print.nebpath . print.profiles . prob . read.hills . read.plumed . summary.fes . summary.hillsfile . summary.minima . summary.nebpath . summary.profiles . tail.hillsfile .
Some associated R codes: RcppExports.R . data.R . minimaandpaths.R . nebs.R . readingandfes.R . Full metadynminer package functions and examples
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