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).

And with its recently released application layer, OpenMM allows non-programmers to easily and quickly run MD simulations and develop custom algorithms on GPUs, while continuing to enable programmers to integrate OpenMM into their own programs.

Workshop Description

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 programming topics will also be covered for those who are interested in them.

During the workshop, participants will gain hands-on experience using OpenMM's new application layer and application programming interface (API). They 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

They will also have time to work with the OpenMM development team on their own research project.

Schedule

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

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.