replica exchange
Posted: 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
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