Defense Date

2009

Document Type

Thesis

Degree Name

Master of Science

Department

Chemical Engineering

First Advisor

MICHAEL PETERS

Abstract

With a modest beginning from developing a model of dynamics of hard liquid spheres (Alder et al., 1957), molecular dynamics (MD) simulations have come to a point where complex biomolecules can be simulated with precision close to reality (Noskov et al., 2007). In this context, a parallel molecular dynamics program for simulation of ion channels associated with cellular membranes has been developed. The parallel MD code developed is simple, efficient, and easily coupled to other codes such as the hybrid molecular dynamics/ brownian dynamics (MD/BD) code developed for the study of protein interactions (Ying et al., 2005). The Atom Decomposition (AD) Method was used in partitioning calculations on atoms to processors. One of the major impediments in using AD was the relatively large size of data that had to be communicated by the processes (Plimpton et al., 1995). Replicating only positions of atoms eased the congestion created by communication of both force terms and positions of atoms between processes. The performance of the code was tested on KcsA, a bacterial potassium channel. The program was written in Fortran 90 with parallel functions from the library of mpich-1.2.7. The idle time of processes was optimized by message driven ordering of communication. The scaling of the parallel program with 2000 – 60,000 atoms was determined and compared with the results obtained from the serial program. As expected, the parallel program scaled better than the serial program as the number of atoms included in the simulation increased from 2000 - 60000. The performance of the parallel program was tested on 4-15 processes, for a system comprising 20,000 atoms. The results obtained were compared with results from the serial program. It was observed that the parallel program scaled better than the serial program as the number of processes increased from 4 to 15. When compared with serial program, which had application of Newton’s Third Law in calculating force terms once per each pair of atoms, it was observed that the parallel program scaled better on 6-15 processes for a physical system comprising of 20,000 atoms.

Rights

© The Author

Is Part Of

VCU University Archives

Is Part Of

VCU Theses and Dissertations

Date of Submission

May 2009

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