Supported Applications

PLUMED

Description

an open source library for free energy calculations in molecular systems that works with some of the most popular molecular dynamics engines. Perform free energy calculations as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation-based steered MD.
Usage
To list all executables provided by PLUMED, run: $ sbgrid-list plumed
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install plumed Available operating systems: Linux 64
Primary Citation*

G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, and G. Bussi. 2014. PLUMED 2: New feathers for an old bird. Computer Physics Communications. 185(2): 604-613.
- *Full citation information available through
Citation Note

Please use the following (or equivalent) wording in any work published using PLUMED: "This work was carried out using the open-source, community-developed PLUMED library, version 2.x (or alternatively version 1.x)." Please visit the PLUMED website for additional citation instructions.
Webinars

Topic: Analyzing and enhancing molecular dynamics simulations with PLUMED
Presenters: Giovanni Bussi -- Associate Professor, SISSA, Trieste, Italy
Massimiliano Bonomi -- Postdoc, University of Cambridge, Vendruscolo Group

Recorded on May 22, 2018
Host: Jason Key