OpenMM Workshop, February 12-13, 2009

Simbios held a two-day workshop on February 12 and 13 to introduce programmers and scientists to two important releases made available mid January on by the Protein Folding group.

1) OpenMM, a high-performance, extensible library written in C++ for executing molecular dynamics (MD) simulations on high performance computer architectures, such as GPUs. Significant performance speed ups of over 100x were achived in some cases using OpenMM.*

Reference code for OpenMM was released in September 08. The January release included a version of Gromacs that uses OpenMM and hence benefits from the speed-up afforded by executing  portions of the code on recent versions of NVIDIA or ATI GPUs. The release supports implicit solvent models, with explicit solvent models to be incorporated into the next release.

2) OpenMM Zephyr, an application that uses Gromacs with OpenMM, and is designed to allow MD novices run Molecular Dynamics simulations and visualize them with VMD.

At the workshop, participants heard from:

  • Experts in molecular dynamics and
  • Representatives from ATI and NVIDIA about their GPU architectures and future plans

OpenMM and OpenMM Zephyr are accelerated only on specific NVIDIA and ATI GPU cards. See list of supported NVIDIA and ATI cards.


  • The first day of the workshop was geared towards developers of molecular simulation code and consisted of a detailed presentation of the API, its integration into Gromacs, including current limitations and future plans, as well as a hands on session exploring integration of OpenMM into AMBER, Desmond, and other MD codes.

  • The second day of the workshop was devoted to researchers using or interested in using Molecular Dynamics simulations, including novices to MD Simulations. We started with an introduction to Molecular Dynamics from experts in the field, followed by a hands-on demo of the current features of the OpenMM Zephyr application. More advanced topics such as force fields, implicit versus explicit solvent with an emphasis on limitations and strengths were discussed in the afternoon.

Detailed Agenda

Logistical Information

Day 1 February 12th 9:30am - 5:00pm, Room S282, Clark Center, Stanford U. (Developer Workshop)
Day 2 February 13th 9:30am - 5:00pm, Room S360, Clark Center, Stanford U. (MD Symposium)

*OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs. conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., in press.