Learning 5 | Beckstein Lab

A tutorial that teaches you to perform and analyze a molecular dynamics simulation of the the enzyme adenylate kinase (AdK) with the Gromacs simulation package.

The script qsub_dependents.py automates the process of submitting strings of dependents jobs. One either tells it how many jobs to run or lets the script calculate the number of jobs based on the benchmarked performance in ns/d and the desired simulation run time in ns. It simplifies running long simulations on supercomputers that limit the run time of jobs.

The course will teach you the theoretical background on how to simulate systems at the atomic scale (e.g. using molecular dynamics), you will learn to program some of the fundamental algorithms, and you will be using state-of-the art software to run simulations of problems in areas of active research. The focus is on bio/nanophysics but there’s room to accommodate individual interests. The course will be half lecture, half hands-on work in a computer lab.

Note that this course is currently not scheduled. It ran the last time in Spring 2013.