Dr. Dobb's | Open Molecular Mechanics (OpenMM) Software Speeds Simulations

Open Molecular Mechanics (OpenMM) Software Speeds Simulations

New open-source software permits faster simulations of molecular motion on desktop computers

February 05, 2009
URL:http://www.drdobbs.com/parallel/open-molecular-mechanics-openmm-software/213201915

A new open-source software package developed at Stanford University is making it possible to do complex simulations of molecular motion on desktop computers at much faster speeds than has been previously possible. "Simulations that used to take three years can now be completed in a few days," said Vijay Pande, an associate professor of chemistry at Stanford University and principal investigator of the Open Molecular Mechanics (OpenMM) project. "With this first release of OpenMM, we focused on small molecular systems simulated and saw speedups of 100 times faster than before."

OpenMM is a collaborative project between Pande's lab and Simbios, the National Center for Physics-based Simulation of Biological Structures at Stanford, which is supported by the National Institutes of Health. The project is described in a paper for the "Early View" section of the Journal of Computational Chemistry.

In the past, researchers needed either supercomputers or large computer clusters to run simulations. Or they had to be content to run only a tiny fraction of the process on their desktop computers. But OpenMM addresses these issues.

The key to the accelerated simulations OpenMM makes possible is the advantage it takes of current graphics processors (GPUs), which cost just a few hundred dollars. At its core, OpenMM makes use of GPU acceleration, a set of advanced hardware and software technologies that enable GPUs, working in concert with the system's central processor (CPU), to accelerate applications beyond just creating or manipulating graphics.

The icing on the molecular-simulation cake is that the software has no allegiance to any particular brand of GPU, and will enable molecular dynamics (MD) simulations to work on most of the high-end GPUs used today in laptop and desktop computers. OpenMM includes a version of the widely used MD package GROMACS that integrates the OpenMM library, enabling it to be sped up on high-end NVIDIA and AMD/ATI graphics cards. Close collaborations with AMD (which owns the ATI brand) and NVIDIA were critical for getting OpenMM to run on their GPUs.

OpenMM incorporates specially developed algorithms that allow MD software to take full advantage of the GPU architecture. In fact, the OpenMM code is at the heart of the GPU implementations of the Folding@home project, which uses the horsepower of GPUs and CPUs in computers around the world to simulate protein folding. The current release uses an implicit solvent model, in which all the surrounding fluid, such as water, is represented as one continuous medium, rather than having each water molecule represented individually (an explicit solvent model). Future releases will allow the modeling of explicit solvent.

A free workshop on OpenMM and OpenMM Zephyr, an easy-to-use application for running and visualizing accelerated MD simulations, will be offered sometime in the next three months. OpenMM is part of Simbios's protein folding research effort and is supported by the National Institutes of Health through the NIH Roadmap for Medical Research Grant U54 GM072970, NSF grant for Cyberinfrastructure (NSF CHE-0535616) and NIH grant on Protein folding (NIH R01-GM062868).