Several algorithms have been used for parallel molecular dynamics, including the replicated algorithm and those based on spatial decompositions. The replicated algorithm stores the entire system's coordinates and forces at each processor, and therefore has a low overhead in maintaining the data distribution. Spatial decompositions distribute the data, providing better locality and scalability with respect to memory and computation. We present EulerGromos, a parallelization of the Gromos molecular dynamics program which is based on a spatial decomposition. EulerGromos parallelizes all molecular dynamics phases, with most data structures using O(N=P ) memory. This paper focuses on the structure of EulerGromos and analyses its performance using molecular systems of current interest in the molecular dynamics community. EulerGromos achieves performance increases with as few as twenty atoms per processor. We also compare EulerGromos with an earlier parallelization of Gromos, UHGromos, wh...

Simulations of interacting particles are common in science and engineering, appearing in such diverse disciplines as astrophysics, fluid dynamics, molecular physics, and materials science. These simulations are often computationally intensive and so natural candidates for massively parallel computing. Many-body simulations that directly compute interactions between pairs of particles, be they short-range or long-range interactions, have been parallelized in several standard ways. The simplest approaches require all-to-all communication, an expensive communication step. The fastest methods assign a group of nearby particles to a processor, which can lead to load imbalance and be difficult to implement efficiently. We present a new approach, suitable for direct simulations, that avoids all-to-all communication without requiring any geometric clustering. For some computations we find the new method to be the fastest parallel algorithm available; we demonstrate its utility...

Molecular dynamics simulation is a class of applications that require reducing the execution time of fixed-size problems. This reduction in execution time is important to drug design and protein interaction studies. Many implementations of parallel molecular dynamics have been developed, but very little work has addressed issues related to the use of machines with 50,000 processors for modest-sized problems in the range of 50,000 atoms. Current massively parallel machines present a major obstacle to achieving good performance: communication overhead. In this paper we quantify the communication latency and network bandwidth necessary to achieve 30--40% efficiency on future message-passing machines with sizes on the order of tens of thousands of processors, for executing molecular dynamics problems with the same order of atoms. We derive an analytical model of a benchmark application that simulates a system of helium atom executing on the Intel Touchstone Delta using an interaction decom...

The ordinary differential equations of Newtonian dynamics are used in atomic simulations with the method of molecular dynamics. The basic issues are surveyed and standard algorithms are described. Several algorithmic variants are discussed. Some advanced ideas relating to parallel computation are considered. Key Words molecular dynamics, atomic simulations, parallel computation Acknowledgements We acknowledge generous support from the National Science Foundation (NSF), award number ASC-9217374 (which includes funds from DARPA), the Grand Challenge Program of the NSF Supercomputer Centers, the Robert A. Welch Foundation, the Texas Coordinating Board and the Alfred P. Sloan Foundation. 1. Introduction Simulations of the atomic motion in chemical and biological systems will play a central role in industrial and medical research and development in the twentyfirst century [1, 3, 13, 15, 16, 20, 31]. New catalysts, pharmaceuticals, and other materials will be designed on computers befor...

Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. Many implementations of parallel molecular dynamics have been developed, but few groups have addressed issues related to the use of massively parallel machines with 100K to 1M processors for small to modest size systems in the range of 50K atoms. This is important for problems in which the goal is to reduce the execution time required to simulate millions of time steps on a modest size problem. In this paper we address two main issues: a good decomposition method that can take advantage of a massively parallel system and the communication requirements needed to achieve 30-40% efficiency on MPPs. We developed an analytical model of a benchmark program that simulates a system with helium atom executing on the Intel Touchstone Delta using an interaction decomposition method. Based upon this model, we ...