— —   Molecular Dynamics for Very Large Systems on Massively Parallel Computers: The MPSim Program KIAN-TAT LIM, 1 SHARON BRUNETT, 2 MIHAIL IOTOV, 1 RICHARD B. MCCLURG, 1 NAGARAJAN VAIDEHI, 1 SIDDHARTH DASGUPTA, 1 STEPHEN TAYLOR, 2 and WILLIAM A. GODDARD III 1 * 1 ( ) Materials and Process Simulation Center, Beckman Institute 139-74 , Division of Chemistry and Chemical Engineering and 2 Scalable Concurrent Programming Laboratory, California Institute of Technology, Pasadena, California 91125 Received 18 August 1995; accepted 12 June 1996 ABSTRACT Ž . We describe the implementation of the cell multipole method CMM in a Ž . Ž . complete molecular dynamics MD simulation program MPSim for massively parallel supercomputers. Tests are made of how the program scales with size Ž . Ž . linearly and with number of CPUs nearly linearly in applications involving up to 10 7 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry.  1997 by John Wiley & Sons, Inc. Introduction arge-scale systems with millions of atoms are L of great interest in many areas of chemistry, biochemistry, and materials science. Such systems *Author to whom all correspondence should be addressed. E-mail wag@wag.caltech.edu This article includes Supplementary Material available from the authors upon request or via the Internet at ftp.wiley.compublicjournalsjccsuppmat18501 or http:www.wiley.comjcc Ž . include viruses such as rhinovirus common cold and poliovirus that contain nearly one million atoms 1 ; starburst dendrimers 2 where self-limited growth of PAMAM may involve molecules with about 250,000 atoms; and commercial polymers where typical molecular weights of 10 million dal- tons would lead to chains with millions of atoms. Ž . Atomistic molecular dynamics MD simulations of such large systems are important to provide the atomic detail needed to specify chemical proper- ties such as binding of a drug to a virus or me- chanical properties such as the modulus. 3 ( ) Journal of Computational Chemistry, Vol. 18, No. 4, 501 521 1997  1997 by John Wiley & Sons CCC 0192-8651 / 97 / 040501-21