Rapid Molecular Dynamics Prototyping
and Simulations on GPUs with OpenMM

Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop.

Introduction to OpenMM

OpenMM is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs) (see benchmarks).

OpenMM has an application layer that allows non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs. It is also a software library, enabling programmers to integrate OpenMM into their own programs.

Workshop Description

Intended Audience: This workshop is designed for those interested in accelerating MD simulations on GPUs and/or developing new MD algorithms that can automatically be implemented and accelerated on GPUs. No programming background is required, though a programming track will be offered for those who are interested in integrating OpenMM into their code.

Flexible Format: A flexible format enables participants to get the most out of the workshop.

  • Separate tracks for developers and molecular dynamics simulation end-users. Register for either Track 1 OR Track 2. Track 3 may be taken independently, or in addition to Track 1 or Track 2.

    Track 1: How to Use OpenMM to Run Molecular Dynamics Simulations
    Those interested in using OpenMM to run simulations will learn to:

    • Set up and run an MD simulation on a GPU using both PDB and AMBER files
    • Create a custom force to apply to their simulations
    • Customize simulations through Python scripting

    Track 2: Integrating OpenMM into My Own Code
    Those looking to integrate OpenMM into an existing code will:

    • Learn how OpenMM has been integrated into other codes
    • Gain insights into the OpenMM design

  • Track 3: Open Research Time: An optional two days are provided for participants to work solely on their own research projects. OpenMM developers and expert users will be available during these optional two working days to consult with participants on their specific issues.

Individuals can attend either the instructional portion or the open working portion or both.


The workshop will be held March 26-29, 2013. Days 1 & 2 of the workshop are instructional. Days 3 & 4 are devoted to working on an individual's research project. Individuals can attend either the instructional portion or the working portion or both.

The agenda for Days 1 & 2 will be determined by participants' interests and backgrounds. A sample agenda is available here.

Workshop Logistics

The workshop will be held at Stanford University and is free to attend. However, registration is required and spaces are limited.

For questions, please send e-mail to


Preparing for the Workshops

For the workshop, attendees are expected to bring their own laptops with the necessary software already installed. Detailed instructions will be sent to participants before the workshops.

Additional details (including directions, travel, & lodging info).

[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]Eastman, P. and Pande, V.S., "Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit," J. Comp. Chem., 2010, 31(6):1268-1272.