Other packages > Find by keyword >

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 21 Nov. 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)
Other packages that cited metadynminer R package
View metadynminer citation profile
Other R packages that metadynminer depends, imports, suggests or enhances
Complete documentation for metadynminer
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA