NAMD2 swMATH ID: 9642 Software Authors: Kale, Laxmikant; Skeel, Robert; Bhandarkar, Milind; Brunner, Robert; Gursoy, Attila; Krawetz, Neal; Phillips, James; Shinozaki, Aritomo; Varadarajan, Krishnan; Schulten, Klaus Description: NAMD2: Greater scalability for parallel molecular dynamics. 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 scalable 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 decomposition to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented 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. par NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications 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. Homepage: http://www.sciencedirect.com/science/article/pii/S0021999199962010 Keywords: biomolecular systems; NAMD2 program Related Software: CHARMM; Gromacs; VMD; NAMD; Globus Toolkit; AMBER; MOIL; GROMOS; WebMO; BioGRID; 3DNA; TK; CHARM++; PVM; OVITO; F2Dock; PFCorr; ZDOCK; NFFT3; Chimera Cited in: 17 Publications all top 5 Cited by 52 Authors 3 Kalé, Laxmikant V. 2 Bhandarkar, Milind 2 Board, John A. jun. 2 Hermans, Jan 2 Schulten, Klaus 2 Skeel, Robert D. 1 Anciaux, Guillaume 1 Bajaj, Chandrajit L. 1 Bała, Piotr 1 Barakos, George N. 1 Bauer, Benedikt 1 Benedyczak, Krzysztof 1 Besseron, Xavier 1 Bettadapura, Radhakrishna 1 Bishop, T. C. 1 Biyikli, Emre 1 Brunger, Axel T. 1 Brunner, Robert J. 1 de Sturler, Eric 1 Dowell, Earl H. 1 Elber, Ron 1 Gautier, Thierry 1 Gonnet, Pedro 1 Gursoy, Attila 1 Heinke, Florian 1 Hoeflinger, Jay P. 1 Krawetz, Neal 1 Labudde, Dirk 1 Li, Aiqin 1 Mann, Geoffrey 1 Molinari, Jean-Francois 1 Nazaruk, Mirosław 1 Nyland, Lars 1 Phillips, James C. 1 Prins, Jan F. 1 Pytliński, Jarosław 1 Schlick, Tamar 1 Seethalakshmi, Arunachalam N. 1 Shinozaki, Aritomo 1 Skorwider, Łukasz 1 Spijker, Peter 1 Steijl, René 1 Stern, Christian 1 To, Albert C. 1 Varadarajan, Krishnan 1 Veluraja, K. 1 Vollrath, Antje 1 Weinbach, Yael 1 Wroński, Michał 1 Wypychowski, Jarosław 1 Yun, R. H. 1 Zhmudsky, O. O. all top 5 Cited in 8 Serials 6 Journal of Computational Physics 1 Computer Methods in Applied Mechanics and Engineering 1 International Journal for Numerical Methods in Fluids 1 New Generation Computing 1 Computational Mechanics 1 SIAM Journal on Scientific Computing 1 Computational & Mathematical Methods in Medicine 1 Journal of Theoretical Biology all top 5 Cited in 8 Fields 8 Biology and other natural sciences (92-XX) 5 Numerical analysis (65-XX) 3 Computer science (68-XX) 3 Mechanics of deformable solids (74-XX) 2 Statistical mechanics, structure of matter (82-XX) 1 Partial differential equations (35-XX) 1 Fluid mechanics (76-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year