Molecular Dynamics for 400 Million Particles with Short-Range Interactions
Yuefan Deng, R. Alan McCoy, Robert B. Marr, Ronald F. Peierls · University of North Texas Digital Library (University of North Texas) · 1995
We report the design and performance of a computational molecular dynamics (MD) code for 400 million particles interacting through the standard pairwise 6--12 Lennard-Jones potential on a 1024-node Intel Paragon, a distributed-memory MIMD parallel computer. The initially recorded "particle-step time" was .4 microseconds. A new inter-node communication strategy ensures high parallel efficiency for a large number of nodes. Besides the ability to tackle large problems, our implementation incorporates a novel method for dynamic load balancing. Our communication and load balancing enhancements provide increased efficiency and flexibility for our MD code, yet are general enough for use in other parallel algorithms. 1 INTRODUCTION Computational molecular dynamics involves the simulation of particles under the influence of inter-particle forces. MD simulations are applicable in many areas, including the study of material properties at the microscopic scale and problems associated with DNApro...