One-day Workshop High-Performance Computing for Molecular Biology

Lecturer: Margaret S. Cheung, Ph.D. Assistant Professor of Physics Contact


Contact phone number: 713-743-8358

Class date and time: April 18th, 2009, Saturday, from 9:30am to 4:30pm

Location: PGH room 200, the University of Houston Registration


deadline: March 27th, first-come-first-serve, up to 20 slots


This one-day workshop will instruct attendants in the use of computational simulations in a high- performance computing environment to study biologically active molecular interactions. The course is a general introduction to computational biology and helps students learn essential software by working on collaborative projects. Students will prepare and execute molecular dynamics simulations, submit job patches to supercomputers using basic commands, analyze the results of the simulations, produce animations, and extract information about the physical and biological functions of the systems under study. Students will have a hand-on experience about how scientists solve complex problems pertinent to real world applications using high- performance computing resources.

Course Organization

Class format is that of a workshop. In the first half of the class the scientific basis of computational simulations for the study of general classes of molecular mechanisms and physics models will be introduced and concepts and techniques for large-scale computing will be discussed. In the second half of the workshop, students will work on individually assigned projects under the lecturers’ guidance. Projects will be related to helix-coil transitions in small proteins.


The class incorporates an on-campus high-performance computing (HPC) resource. Students will have free access to HPC to which they will submit their molecular simulations in forms of patch jobs. Personal computers will be available for each student in the computer classrooms in order to display and analyze the results of the simulations and compare HPC performances


  • Professor Margaret Cheung’s research group
  • UH/Rice
  • Quarknet
  • Texas Learning and Computation Center
  • Department of Physics at the University of Houston