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I'd like to align ~2000 molecules consisting of 8 atoms of carbon and evaluate their similarity with RMSD (all vs all molecules).

What open software can do it in a day or less? I'd like it to work on Ubuntu, and if possible that it calculates the alignments in parallel.

My files are xyz: number of atoms, element+coordinates of each atom.

Thank you.

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Assuming you know basic coding and are able to write a simple script doing the input and writing the output for all the 4 million calculations you can use for example this script I found some days ago for doing the alignment and RMSD calculation. Alternatively PyMol can do this too (align function).

Not quite sure about the timing*, even if one would take a second, I expect it to be much faster, that's still about two days if run in sequence. If you are doing this only once it might not be worth the effort to optimize this and I'd rather wait some hours or days or run several of those jobs in parallel on a cluster.

*I've made a similar script and reading the xyz files, calculating the RMSD and even saving the aligned structures takes about 5 ms, which means it's done in less than 6 hours even without running it in parallel.

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    $\begingroup$ The rmsd package is nice, yes. $\endgroup$ – pH13 - Yet another Philipp May 14 '18 at 4:54
  • $\begingroup$ A good idea to get this working in parallel would be to write a Python script that calls rmsd with multiprocessing, rather than using xargs or GNU parallel from the command line. $\endgroup$ – pentavalentcarbon May 14 '18 at 14:55

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