High-Performance Molecular Dynamics

Computer Science and Geological Sciences
Spring 1995

Molecular dynamics is an increasingly important scientific tool with lots of applications in areas such as chemistry and geology. Computational molecular dynamics simulates the behavior of a physical system by computing the interaction between particles at the molecular level, according to a mathematical model of their interaction. This "n-body problem" also can be found in astronomy. For a large number of particles, the computational requirements are tremendous. High-performance computers, such as massively parallel machines, promise to considerably speed up this computation.

In this seminar, we study the computational issues involved in molecular dynamics, such as geological applications, force calculations, the Barnes-Hut algorithm, the Fast Multipole Method, visualization, parallelization, and portability.

Prerequisites: Graduate Standing or consent of an instructor
Enrollment code: GCMPS 595I: 63008; GEOL 270B: TBA
Units: 1
Grades: Pass/Fail
Meetings: Room: GEOL 1006, Time: Tuesday, 9:30 - 10:45
Course organization: We read and present recent papers from conferences and journals. Each student presents at least one paper.



Our goal is to learn the computational aspects of molecular dynamics (MD) well enough to create, or competently critique, an NSF research proposal.



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Last modified: Wed Mar 29 15:53:56 PST 1995 by Pete Cappello