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Mega-molecular dynamics on highly parallel computers : methods and applications


Lim, Kian-Tat (1995) Mega-molecular dynamics on highly parallel computers : methods and applications. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/e3qc-t131.


Large-scale systems of thousands and millions of atoms are of great interest in many areas of chemistry, biochemistry, and materials science. Atomic-level simulations of such systems can provide increased accuracy and especially enhanced insight and understanding when compared with either smaller-scale model calculations or grossly-averaged macroscopic models.

Megamolecular simulations require large amounts of memory and computation, far more than can be provided by the typical scientific workstation. These resources can be most cost-effectively provided at this time by scalable massively parallel computers.

This thesis presents a large-scale, parallel, distributed-memory, general-purpose molecular dynamics code. The most time-consuming portion of the calculation, the computation of the nonbonded forces, is handled by the Cell Multipole Method, which was developed to overcome the speed and accuracy limitations of standard techniques for handling long-range power-law interactions in large molecular systems. Versions of the code for the KSR-1 and Intel Delta and Paragon parallel supercomputers are described, and performance, accuracy, and scalability results are given.

The applications section begins with a discussion of computational experiments leading to a prescription for choosing the value of the free timescale parameter in Nose-Hoover constant-volume, constant-temperature (NVT) canonical dynamics. This is followed by several applications of the above megamolecular dynamics codes to interesting chemical applications in the areas of argon cluster structure, polymer structure, surface tension of water drops, diffusion of gases through polymers, and viral structure.

Item Type:Thesis (Dissertation (Ph.D.))
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Goddard, William A., III
Thesis Committee:
  • Goddard, William A., III (chair)
Defense Date:27 April 1995
Record Number:CaltechETD:etd-10152007-143016
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:4103
Deposited By: Imported from ETD-db
Deposited On:26 Oct 2007
Last Modified:16 Apr 2021 22:32

Thesis Files

PDF (Lim_kt_1995.pdf) - Final Version
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