Learning 4 | Beckstein Lab

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Tutorial: MDAnalysis

Tutorial: MDAnalysis

A short introductory tutorial on MDAnalysis

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Tutorial: Simulating AdK with Gromacs

Tutorial: Simulating AdK with Gromacs

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.

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Submitting strings of jobs on supercomputers

Submitting strings of jobs on supercomputers

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.

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