CMSC6920 Scientific Programming Winter 2011

Module I: Molecular Dynamics Simulation

Module I runs from January 7 to February 2, inclusive.

Instructor: Ivan Saika-Voivod, Office: C1059, phone: 864-8886, email: saika@mun.ca

Course website: http://www.physics.mun.ca/~saika/CMSC6920/

The course D2L shell will be used to post marks

Overview: Students will learn about molecular dynamics (MD) simulation theory and
practice. Topics include structure of an MD simulation, calculating various physical
quantities and error estimates, integration algorithms, neighbour lists, rigid bodies, long-
range interactions and simulations at constant temperature and pressure.

Classes: Monday, Wednesday and Friday 3:00-3:50 pm, room C3067

Labs: a 2-hour lab slot will be scheduled

Programming experience: Students should be familiar with coding Fortran or C in a

Unix-like environment. Sample codes are written in Fortran. Some workshop-type
material will be presented in Mathematica.

Recommended Textbooks: Understanding Molecular Simulation: From Algorithms to

Applications, D. Frenkel and B. Smit (Academic Press); Computer Simulation of Liquids,
M.P. Allen and D.J. Tildesley, (Oxford University Press).

Evaluation:
• 80% Project
• 20% Assignment Questions