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shirtsgroup / cg_openmm

Tools to build coarse grained models and perform simulations with OpenMM
MIT License
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replace distance calculations with mdtraj #64

Open cwalker7 opened 4 years ago

mrshirts commented 4 years ago

I think this sounds like a good idea, though there will have to be some analysis of where it is used, and then restructured so it is done in array form all in mdtraj, rather than looping in pure Python and doing distances of individual pairs - will be much faster that way.

cwalker7 commented 4 years ago

Transferred this here because I think it's most relevant for the native contacts calculation.

As it is now, the native contacts code is very slow (about 0.3 second per frame of a 48-particle system) - this means about 15 hours for a 36 replica system with 5000 frames each. We may want to update the distance calculations now - I can get started on it to see if I can get any better speed.

mrshirts commented 4 years ago

I think this makes sense to look at. You can be testing other systems for heat capacity/etc. while implementing this. I suspect it could be sped up a fair amount with mdtraj, but mdtraj will probably be much faster in the end.