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

February 05, 2009

Whether vibrating in place or taking part in protein folding to ensure cells function properly, molecules are never still. Simulating molecular motions provides researchers with information critical to designing vaccines and helps them decipher the bases of certain diseases, such as Alzheimer's and Parkinson's, that result from molecular motion gone awry.

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 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 that was scheduled to be posted online Feb. 3 in the "Early View" section of the Journal of Computational Chemistry.

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, meaning it is, as computer geeks like to say, "brand agnostic." OpenMM will enable molecular dynamics (MD) simulations to work on most of the high-end GPUs used today in laptop and desktop computers.

This is a boon to MD developers. Converting their code to run on just one GPU product is a challenging project by itself. And until now, if developers wanted to accelerate their MD software on different brands of GPUs, they would have to write multiple versions of their code. OpenMM provides a common interface.

"OpenMM will allow researchers to focus on the science at hand instead of the hardware," Pande said. "Researchers will see a jump in productivity and resourcefulness from computers they already own." With OpenMM, researchers can use GPUs to perform massively parallel calculations.

OpenMM fits squarely with Simbios' mission of providing computational tools to stimulate research in biology and medicine, according to Russ Altman, principal investigator of Simbios and chair of the Department of Bioengineering at Stanford. "OpenMM will be a tool that unifies the MD community," he said. "Instead of difficult, disparate efforts to recode existing MD packages to enjoy the speedups provided by GPUs, OpenMM will bring GPUs to existing packages and allow researchers to focus on discovery."

The new release of 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.

"Cross-platform solutions like OpenMM enable a much broader community of researchers to leverage GPU acceleration capabilities like ATI Stream technology" said Patricia Harrell, director of Stream Computing, AMD. "AMD is committed to supporting open, cross platform tools that allow researchers to focus on solving problems with their GPU of choice."

NVIDIA is similarly committed to OpenMM. "OpenMM promises to further increase the adoption of GPU technology among the molecular dynamics community," said Andy Keane, general manager, GPU Computing at NVIDIA. "We'll continue our close collaboration with Stanford on OpenMM so that current and future libraries can maximally leverage the power of the GPU."

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.

Stanford University

Introduction to Molecular Motion in Polymers
by Richard A. Pethrick (Author), Taweechai Amornsaichai (Author), Alastair M. North (Author)

This book explains how molecular movement is determined by chemical structure, then how motion controls the physical and technological properties of polymer materials. Readers are introduced to the concepts of molecular movement in polymers and the connections with causative chemical structure on the one hand and resulting bulk physical and technological behavior on the other. The approach is non-mathematical, but is molecularly based and allows readers to understand the detailed chemical and rigorous mathematical discussions of more advanced texts.

NMR Studies of Translational Motion: Principles and Applications (Cambridge Molecular Science)
by William S. Price (Author)

Translational motion in solution, either diffusion or fluid flow, is at the heart of chemical and biochemical reactivity. Nuclear Magnetic Resonance (NMR) provides a powerful non-invasive technique for studying the phenomena using magnetic field gradient methods. Describing the physical basis of measurement techniques, with particular emphasis on diffusion, balancing theory with experimental observations and assuming little mathematical knowledge, this is a strong, yet accessible, introduction to the field. A detailed discussion of magnetic field gradient methods applied to Magnetic Resonance Imaging (MRI) is included, alongside extensive referencing throughout, providing a timely, definitive book to the subject, ideal for researchers in the fields of physics, chemistry and biology.

Spectroscopic Techniques and Hindered Molecular Motion
by Ferid Bashirov (Author)

Spectroscopic Techniques and Hindered Molecular Motion presents a united, theoretical approach to studying classical local thermal motion of small molecules and molecular fragments in crystals by spectroscopic techniques. Mono- and polycrystalline case studies demonstrate performance validity. The book focuses on small molecules and molecular fragments, such as N2, HCl, CO2, CH4, H2O, NH4, BeF4, NH3, CH2, CH3, C6H6, SF6, and other symmetrical atomic formations, which exhibit local hindered motion in molecular condensed media: molecular and ionic crystals, molecular liquids, liquid crystals, polymeric solids, and biological objects. It reviews the state of studying the hindered molecular motion (HMM) phenomenon and the experimental works on the basis of the latest theoretical research....

Polymer Materials: Macroscopic Properties and Molecular Interpretations
by Jean Louis Halary (Author), Francoise Laupretre (Author), Lucien Monnerie (Author)

Advanced reviews for Polymer Materials"Molecular modeling of polymers ... is a subject that cannot be found in any other [book] in any appreciable detail. ... [T]he detailed chapters on specific polymer systems is a great idea."— Gregory Odegard, Michigan Technological University"The polymer community needs a text book which can connect the macroscopic mechanics with mesoscopic and molecular aspects of polymer."— Liangbin Li, University of Science and Technology of ChinaThis book takes a unique, multi-scale approach to the mechanical properties of polymers, covering both the macroscopic and molecular levels unlike any other book on the market. Based on the authors’ extensive research and writing in the field, Polymer Materials emphasizes the relationships between the chemical...

Molecular Biophysics: Structures in Motion
by Michel Daune (Author), W. J. Duffin (Translator), David Blow (Translator)

Offering a comprehensive introduction to the molecular physics of biological systems, this book seeks to explain how the laws and concepts of physics apply to the living world at the molecular and subecellular level, with an emphasis on electrical and dynamical behavior. It is organized into five parts: conformation of biopolymers; dynamics of biopolymers; hydration of biopolmers; biopolymers as polyelectrolytes; and association between molecules.

Molecular Motion in High Polymers (International Series of Monographs on Chemistry)
by R. T. Bailey (Author), Alistair M. North (Author), Richard A. Pethrick (Author)

Presents an up-to-date view of the ways in which the molecular dynamics of poylmers affect a variety of macroscopic phenomena.

Protein Motions (Molecular Biology Intelligence Unit)
by S. Subbiah (Author)

This book reveals the spectacular degree to which biological macromolecules, particularly proteins, move as they go about their business. The first chapters of the book deal with methods and computer algorithms, both subjective and objective, that have been historically used to analyze the changes when two alternate conformations are known. The following chapters present classification schemes to catalogue these changes. The final chapters discuss in detail several notable examples of dynamic protein motion by specialists in those areas. This book includes an interactive multimedia CD-ROM, which depicts the motions of seven proteins in Molscript, c-alpha and CPK and describes the nature of their molecular hinge mechanisms.

Quantum Aspects of Molecular Motions in Solids: Proceedings of an ILL-IFF Workshop, Grenoble, France, September 24-26, 1986 (Springer Proceedings in Physics)
by Anton Heidemann (Editor), Andreas Magerl (Editor), Michael Prager (Editor), Dieter Richter (Editor), Tasso Springer (Editor)

Cell and Molecular Biology: Concepts and Experiments (Karp, Cell and Molecular Biology)
by Gerald Karp (Author)

Karp continues to help biologists make important connections between key concepts and experimentation. The sixth edition explores core concepts in considerable depth and presents experimental detail when it helps to explain and reinforce the concepts. The majority of discussions have been modified to reflect the latest changes in the field. The book also builds on its strong illustration program by opening each chapter with “VIP” art that serves as a visual summary for the chapter. Over 60 new micrographs and computer-derived images have been added to enhance the material. Biologists benefit from these changes as they build their skills in making the connection.

Cellular and Molecular Immunology: with STUDENT CONSULT Online Access, 7e (Abbas, Cellular and Molecular Immunology)
by Abul K. Abbas MBBS (Author), Andrew H. Lichtman MD PhD (Author), Shiv Pillai MD (Author)

Cellular and Molecular Immunology takes a comprehensive yet straightforward approach to the latest developments in this active and fast-changing field. Drs. Abul K. Abbas, Andrew H. Lichtman, and Shiv Pillai present sweeping updates in this new edition to cover antigen receptors and signal transduction in immune cells, mucosal and skin immunity, cytokines, leukocyte-endothelial interaction, and more. In print and online with additional resources, this reference is the up-to-date and readable textbook you need to master the complex subject of immunology.Access to www.studentconsult.com and Evolve provides informative lecture slides based on images in the book, fully modified for incorporation into your lesson plans. Other online features include searchable text, an image bank,...