Journal of Computational Physics 151, 283–312 (1999) Article ID jcph.1999.6201, available online at http://www.idealibrary.com on NAMD2: Greater Scalability for Parallel Molecular Dynamics Laxmikant Kal´ e, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten Theoretical Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801 E-mail: kale@ks.uiuc.edu Received July 20, 1998; revised December 28, 1998 Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scal- able program. It is also necessary that the program be easily modified by application– domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decom- position to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and im- plemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applica- tions can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. c  1999 Academic Press 1. INTRODUCTION AND MOTIVATION Molecular dynamics (MD) serves a pivotal role in inferring functions of biomolecules from their structures. The number of structures obtained via X-ray crystallography and other means has increased tremendously in the past several years. Researchers believe that molecular dynamics simulations are critical in translating structure information into mechanisms underlying biomolecular functions. Successful simulations of biomolecular 283 0021-9991/99 $30.00 Copyright c  1999 by Academic Press All rights of reproduction in any form reserved.