cheng7258002/vmd_plumed

Main code repository for the PLUMED-GUI plugin for VMD

Plumed-GUI

Toni Giorgino
Consiglio Nazionale delle Ricerche (IN-CNR)

A Plumed 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 tonigi/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 (please read and cite)
  • Toni Giorgino, Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts (2014) Computer Physics Communications, Volume 185, Issue 3, March 2014, Pages 1109-1114, doi:10.1016/j.cpc.2013.11.019, or arXiv:1312.3190
• Information on the PLUMED engine at http://www.plumed.org

Citation

You are kindly requested to cite the following paper in any publication resulting from the use of Plumed-GUI (in addition to other possibly relevant Plumed citations):

• Toni Giorgino, Plumed-GUI: an environment for the interactive development of molecular dynamics analysis and biasing scripts (2014) Computer Physics Communications, doi:10.1016/j.cpc.2013.11.019 or http://arxiv.org/abs/1312.3190 .