replica exchange

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Drew Thomson
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Joined: Fri Jul 13, 2018 5:58 am

replica exchange

Post by Drew Thomson » Fri Jul 13, 2018 6:06 am

Hi all

I am comparatively new to MD simulations, and am at the stage of being able to run conventional MD simulations of my systems of interest (fairly small peptides, sometimes with non-natural residues). I am using Amber forcefields and running in openMM via a jupyter notebook. I know from experimental studies that one of my peptides exhibits a cis-trans isomerisation at a proline residue, and was hoping to probe this in MD using some sort of enhanced sampling method, possibly replica exchange.

Does anyone have any experience of setting this sort of simulation up in openMM? I'm a comparative newbie, so a gist would be a massive help. Any pointers would be much appreciated!

Drew
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Peter Eastman
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Joined: Thu Aug 09, 2007 1:25 pm

Re: replica exchange

Post by Peter Eastman » Fri Jul 13, 2018 9:50 am

OpenMMTools includes an implementation of replica exchange. See https://openmmtools.readthedocs.io/en/latest/. There's also an implementation of simulated tempering, which is a related sampling method, at https://simtk.org/plugins/moinmoin/open ... Repository.
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