I work in the area of classical molecular dynamics (MD). It's an atomistic simulation method where:
I've worked on several parallel algorithms that are useful for MD simulations. They are described in the next section.
I've also written several parallel MD codes that I distribute freely. They are available from this page.
Performance of these parallel codes for a variety of systems (atomic, polymer, biomolecular, metal, granular) on several parallel platforms are discussed on the Benchmark page of the LAMMPS WWW Site.
Simulation efforts that I've been involved in are discussed on this page. Work of others using these codes is listed on the Publications page of the LAMMPS WWW Site, along with pictures and movies.
This paper describes 3 classes of parallel algorithms suitable for short-range MD force fields: so-called atom-, force-, and spatial-decomposition algorithms. All 3 are implemented and compared in the paper, but the only one I "invented" was force-decomposition which was work with Bruce Hendrickson at Sandia.
In a nutshell, atom-decomposition methods assign a subset of atoms permanently to each processor, force-decomposition methods assign a subset of pairwise force computations to each proc, and spatial-decomposition methods assign a sub-region of the simulation box to each proc.
Fast Parallel Algorithms for Short-Range Molecular Dynamics, S. J. Plimpton, J Comp Phys, 117, 1-19 (1995). (abstract) (postscript) (ps.gz) Some postscript viewers will not display figures in this paper properly - here is a separate tar file of the figures.
The Lennard-Jones codes discussed in the paper that implement the various parallel algorithms are available for download here.
This paper describes the pros and cons of the 3 algorithms in the context of molecular systems, where one must also compute intra-molecular forces - e.g. bond, angle, torsional terms within each molecule's topology.
Parallel Molecular Dynamics Algorithms for Simulation of Molecular Systems, S. J. Plimpton and B. A. Hendrickson, chapter in Parallel Computing in Computational Chemistry, edited by T. G. Mattson, published by the American Chemical Society, Symposium Series 592, 114-132 (1995). (abstract) (postscript) (ps.gz)
This paper describes how to use the force-decomposition algorithm with embedded atom method (EAM) potentials which are commonly used for metals and alloy systems. We implemented the idea in a code called ParaDyn, which is a parallelization of the serial DYNAMO EAM code of Stephen Foiles and Murray Daw, and which is available for download here.
Parallel Molecular Dynamics With the Embedded Atom Method, S. J. Plimpton and B. A. Hendrickson, in Materials Theory and Modelling, edited by J. Broughton, P. Bristowe, and J. Newsam, MRS Proceedings 291, Pittsburgh, PA, 1993, p 37. (abstract) (postscript) (ps.gz)
The extension of the force-decomposition idea to molecular MD is described in this paper. We used these ideas in a Sandia code called ParBond; it has since been superceded by our LAMMPS code.
A New Parallel Method for Molecular-Dynamics Simulation of Macromolecular Systems, S. J. Plimpton and B. A. Hendrickson, J Comp Chem, 17, 326-337 (1996). (abstract) (postscript) (ps.gz)
LAMMPS is our current production-scale molecular MD code (suitable for molecular or atomic systems). Two of its parallel algorithms are discussed in this paper.
Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN, March 1997. (abstract) (postscript) (ps.gz)
This paper discusses projections of what will be possible with classical MD using current techniques on high-end computers of the future.
Computational Limits of Classical Molecular-Dynamics Simulations, S. J. Plimpton, Computational Materials Science, 4, 361-364 (1995). (abstract) (postscript) (ps.gz)