Tag Archives: Parallel computing

The stuff MDAnalysis didn’t implement: CPU Parallel HOLE conductance analysis

Some time ago, I needed to find a way to computationally estimate conductance values for every protein frame from several molecular dynamics (MD) trajectories.

In a previous post, I wrote about how to clean the resulting instant conductance timeseries from outliers. But, I never described how I generated these timeseries.

In this post, I will show how you can parallelise the computation of instant conductance given an MD trajectory. I will touch on the difficulties of this process. And why I had to implement a custom tool for it given that MDAnalysis seems to already have implemented a routine of this sort. Finally, I will provide two Python scripts that you can easily adapt to run your parallel calculations – for which I’ll provide some important notes you don’t wanna skip.

Violin plots of conductance distributions from 64 molecular dynamic trajectories with 1000 frames each.
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