Pathways plugin in a nutshell

This repository includes the current version of code, documentation, and usage examples of the Pathways plugin for VMD described in the 2012 J. Comp. Chem. article. My old Pathways page at Duke University that the article links to will no longer be updated or maintained, nor will I respond to emails to my former Duke University address. (Actually, the old page has not been updated for a while, largely because of Duke requiring to use a non-standard closed-source client for VPN access). Please contact me on Github instead, if needed.

Repository structure:

/---
   |--- 1bex_wt_movie   (example for an MD trajectory with generating a pathway animation)
   |--- images   (images included in README.html)
   |--- install_vmdstore.txt   (info for VMD store (https://biosim.pt/how-to-install-vmd-store))
   |--- install_windows.md   (installation instructions for Windows)
   |--- LICENSE   (GPL v.3 or later)
   |--- pathways ---   (code for Pathways plugin and pathcore executable)
   |                |--- collective.tcl
   |                |--- pathways.tcl
   |                |--- pkgIndex.tcl
   |                |--- pathcore ---
   |                                 |--- bin ---   (binary executables for different platforms)
   |                                 |           |--- pathcore_x86-64.zip
   |                                 |           |--- pathcore_i386.zip
   |                                 |           |--- pathcore_windows.zip
   |                                 |           |--- pathcore_darwin.zip
   |                                 |--- src ---   (source code for different platforms)
   |                                             |--- Linux_MacOS
   |                                             |--- Windows
   |--- README.html   (theory|documentation page)
   |--- README.md   (this file)

Documentation

The old theory|documentation page, including installation instructions, is in README.html. To browse it, please clone the repository and open the file locally on your computer.

Installation

Installation instructions for Linux and MacOS are included into the documentation page. Installation instructions for Windows are in install_windows.md.

Usage examples

Directory 1bex_wt_movie includes a complete example of a Pathways plugin run on an MD trajectory with generating a video animation of pathway dynamics. Example output files are included.

Credit

If you find Pathways helpful, please cite the article:

Balabin, I. A., Hu, X., & Beratan, D. N. (2012). Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD. J. Comp. Chem. 33(8), 906–910.

(DOI https://doi.org/10.1002/jcc.22927)