Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers

Mark Tuckerman, D. A. Yarne, Shane O. Samuelson, Adam L. Hughes, Glenn J. Martyna

Research output: Contribution to journalArticle

Abstract

Modern Molecular Dynamics methods are employed to study quantum manybody systems, chemically reactive systems including explicit electronic degrees of freedom, and combinations thereof, as well as large classical biomolecular systems. Thus, complex problems such as isotope effects on enzymatic reactions can now be examined, routinely. In this article, modern molecular dynamics methods are reviewed and their application to quantum manybody systems and electronic structure calculations described. The resulting methodology, however, while powerful, is computationally intensive. Therefore, the mathematical structure of the techniques has been exploited to develop distributed memory parallel algorithms employing multiple levels of discretization. These multilevel-parallel methods are efficient and permit the large complex systems, such as enzyme catalysis, to be treated easily. In addition, it is shown how modern object oriented programming paradigms can be employed to implement multilevel parallel algorithms in a large computational package rapidly and efficiently. Finally, results and timings obtaining using the PINY_MD package developed by the authors are given for a variety of novel systems.

Original languageEnglish (US)
Pages (from-to)333-376
Number of pages44
JournalComputer Physics Communications
Volume128
Issue number1
DOIs
StatePublished - Jun 9 2000

Fingerprint

distributed memory
memory (computers)
Parallel algorithms
Molecular dynamics
object-oriented programming
molecular dynamics
computer programs
Data storage equipment
Object oriented programming
complex systems
isotope effect
Catalysis
catalysis
Isotopes
Electronic structure
enzymes
Large scale systems
Enzymes
degrees of freedom
time measurement

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy(all)

Cite this

Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers. / Tuckerman, Mark; Yarne, D. A.; Samuelson, Shane O.; Hughes, Adam L.; Martyna, Glenn J.

In: Computer Physics Communications, Vol. 128, No. 1, 09.06.2000, p. 333-376.

Research output: Contribution to journalArticle

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