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Plumed-GUI

Toni Giorgino

A collective variable analysis tool for VMD

The PLUMED-GUI collective variable analysis tool is a plugin for the Visual Molecular Dynamics (VMD) software that provides access to the extensive set of collective variables (CV) defined in the PLUMED. It allows you to:

  • analyze the currently loaded trajectory by evaluating and plotting arbitrary CVs
  • use VMD's atom selection keywords to define atom groups and ready-made templates for common CVs
  • export the CV definition file for use in MD simulations
  • prepare reference files for RMSD, path-variable, native contacts, etc.

The code is hosted on GitHub at giorginolab/vmd_plumed.

Installation

First, you need PLUMED 1.3's driver and/or PLUMED 2's plumed executables: see INSTALL-PLUMED-FIRST.md.

Second, you may want to update PLUMED-GUI to its latest version, rather than using the one distributed with VMD. See instructions in INSTALL.md.

Documentation

Please find

  • A short manual and quickstart in the doc/README.md file
  • An extensive description in the accompanying paper (see the Citation section): Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts doi:10.1016/j.cpc.2013.11.019
  • Information on the PLUMED engine at http://www.plumed.org

Citation

If you use Plumed-GUI in research work, please cite the following paper (in addition to other possibly relevant Plumed citations):

  • T. Giorgino, “PLUMED-GUI: An environment for the interactive development of molecular dynamics analysis and biasing scripts,” Computer Physics Communications, vol. 185, no. 3, pp. 1109–1114, Mar. 2014. doi:10.1016/j.cpc.2013.11.019 and arXiv:1312.3190