CRAN

metadynminer 0.1.4

Tools to Read, Analyze and Visualize Metadynamics HILLS Files from 'Plumed'

Released Mar 13, 2019 by Vojtech Spiwok

This package can be loaded by Renjin but 9 out 36 tests failed.

Dependencies

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.

Installation

Maven

This package can be included as a dependency from a Java or Scala project by including the following your project's pom.xml file. Read more about embedding Renjin in JVM-based projects.

<dependencies>
  <dependency>
    <groupId>org.renjin.cran</groupId>
    <artifactId>metadynminer</artifactId>
    <version>0.1.4-b1</version>
  </dependency>
</dependencies>
<repositories>
  <repository>
    <id>bedatadriven</id>
    <name>bedatadriven public repo</name>
    <url>https://nexus.bedatadriven.com/content/groups/public/</url>
  </repository>
</repositories>

View build log

Renjin CLI

If you're using Renjin from the command line, you load this library by invoking:

library('org.renjin.cran:metadynminer')

Test Results

This package was last tested against Renjin 0.9.2724 on Mar 15, 2019.

Source

C++

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