Reactive Dynamics Tutorial

As part of the virtual Winterschool on Computational Chemistry, I gave a presentation outlining the methods that we’ve been developing over the past few years which enable folks to carry out reactive dynamics using the multi-state empirical valence bond (MS-EVB) method. Taking advantage of the fact that I could deliver the virtual lecture from the comfort of my own command line, I took the opportunity to guide viewers through a tutorial on how to use the MS-EVB functionality that we’ve implemented within a branch of the TINKER molecular dynamics package that I initiated with Jeremy Harvey a few years ago. This project, which is hosted on SourceForge and available for download, is effectively an OpenMPI parallelized version of TINKER, which is molecular dynamics package distributed by Jay Ponder’s lab at Washington University in St. Louis. I regularly get email requests from folks who are studying reaction dynamics asking to use this stuff, so I have included video links to the presentation in case they are of use to others. The presentation is in two parts:

Part 1 outlines the types of systems that we have studied to date using our MS-EVB reactive dynamics codes, and a brief discussion of some of the insights and results from that work.

Part 2 describes how to build the MPI-parallelized version of TINKER, along with several examples of how to run it. These include: geometry optimizations (TS & minima), frequency calculations, single point energy calculations, and an NVE molecular dynamics simulation.

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