Chicago (IL) - Yesterday, Stanford released Open Molecular Mechanics version 1.0. The software library is designed to greatly accelerate molecular computations through a standard library of simulation and advanced GPU utilization. OpenMM will allow simulations to run 100 times faster than was previously possible without GPU abilities.





Said Vijay Pande, an associate professor of chemistry at Stanford, "Simulations that used to take three years can now be completed in a few days. 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 large endeavor supported by Pande's lab, Simbios, the National Center for Physics-based Simulation of Biologic Structures-Stanford and the National Institutes of Health. The work is published in the February 3 Early View section of the Journal of Computational Chemistry.



The new release of OpenMM includes a version of the widely used MD package GROMACS, which integrates the OpenMM library and enables it to be sped up on high-end GPU cards like those from NVIDIA and AMD/ATI. AMD and NVIDIA both helped significantly in making sure this software ran effectively and efficiently on their GPUs.



From the press release:

"A free workshop on OpenMM and OpenMM Zephyr (http://simtk.org/home/zephyr), an easy-to-use application for running and visualizing accelerated MD simulations, will be offered sometime in the next three months. Anyone interested in learning about using OpenMM and OpenMM Zephyr will be welcome. A workshop on Feb. 12 is already filled. For more information on the workshop, or a symposium on molecular dynamics held the day after each workshop, email simbiosfeedback@stanford.edu.

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). Information on the National Centers for Biomedical Computing can be obtained from http://nihroadmap.nih.gov/bioinformatics. To learn more about Simbios and its research and software tools, visit http://simbios.stanford.edu."