Molecular Dynamics Workshop Series, June 24-26, 2009

Simbios is excited to announce its Molecular Dynamics Workshop Series. The series consistsed of three workshops, showcasing software designed for individuals with different interests and experience with molecular dynamics (MD), from novices to experts.

  • OpenMM Developers Workshop: Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations.[1] The workshop highlighted the explicit solvent capabilities that is available OpenMM and includes a special track focused on integration of OpenMM into AMBER.
  • Introduction to Markov State Models and MSMBuilder: For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. Participants learned about Markov State Models and why they are suitable for this, and use the MSMBuilder software[2] to automatically construct such models, as well as analyze and visualize them.
  • Introduction to Molecular Dynamics and OpenMM Zephyr: For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.

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


  • June 24-26: OpenMM Developers Workshop (detailed agenda)

    • Day 1 presents lectures and hands-on exercises that introduce attendees to the OpenMM API, highlighting the basic framework and the explicit solvent capabilities. In the afternoon, participants can choose from two tracks: integrating OpenMM into your custom code or integrating OpenMM into AMBER.
    • Days 2-3 are provided for participants to continue working on the OpenMM integration with assistance from the OpenMM developers. (optional)

  • June 25: Introduction to Markov State Models and MSMBuilder (detailed agenda)

    • Introduction to Markov State Models and their applications
    • Hands-on tutorials using MSMBuilder to analyze small datasets
    • Help with using MSMBuilder to analyze your own data

  • June 26: Introduction to Molecular Dynamics and OpenMM Zephyr (detailed agenda)

    • Introduction to molecular dynamics
    • Hands-on tutorial on using OpenMM Zephyr
    • Hands-on tutorial on using OpenMM Zephyr and mdrun_openmm to more quickly and easily set up and run custom simulations beyond those available through Zephyr

Workshop Series Materials

Click here to access the slides, videos and other materials from the workshop.

[1] 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., 2009, 30(6):864-872.
[2] GR Bowman, X Huang, and VS Pande, "Using generalized ensemble simulations and Markov state models to identify conformational states," Methods (accepted).