Educational aspects of molecular simulation

Abstract

This article addresses some aspects of teaching simulation methods to undergraduates and graduate students. Simulation is increasingly a cross-disciplinary activity, which means that the students who need to learn about simulation methods may have widely differing backgrounds. Also, they may have a wide range of views on what constitutes an interesting application of simulation methods. Almost always, a successful simulation course includes an element of practical, hands-on activity: a balance always needs to be struck between treating the simulation software as a ‘black box’, and becoming bogged down in programming issues. With notebook computers becoming widely available, students often wish to take away the programs to run themselves, and access to raw computer power is not the limiting factor that it once was; on the other hand, the software should be portable and, if possible, free. Examples will be drawn from the author's experience in three different contexts. (1) An annual simulation summer school for graduate students, run by the UK CCP5 organization, in which practical sessions are combined with an intensive programme of lectures describing the methodology. (2) A molecular modelling module, given as part of a doctoral training centre in the Life Sciences at Warwick, for students who might not have a first degree in the physical sciences. (3) An undergraduate module in Physics at Warwick, also taken by students from other disciplines, teaching high performance computing, visualization, and scripting in the context of a physical application such as Monte Carlo simulation.

Keywords:

• Simulation
• Education
• Training

Acknowledgements

It is a pleasure to acknowledge the huge contribution made by my colleagues, Dominic Tildesley and Julian Clarke, to the creation and running of the CCP5 Spring School between 1994 and 2001. Bill Smith, and many others too numerous to mention, also gave valuable support over the years. Funding for the school was provided by EPSRC, the Royal Society of Chemistry Statistical Mechanics and Thermodynamics Group, the ESF program SIMU, and EU Marie Curie Actions. The assistance of David Cheung in supervising the MOAC workshops, and John Grime in supervising the HPC course workshops, is gratefully acknowledged. Funding for MOAC, and for the Warwick HEC training centre, was provided by EPSRC. NAMD and VMD were developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. The computing facilities for courses at Warwick were provided by the Centre for Scientific Computing of the University of Warwick, with the support of the system administrators Matt Ismail and Jaroslaw Zachwieja, and additional facilities provided by IT Services.