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

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.

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.

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 simbiosfeedback@stanford.edu.

Preparing for 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.