From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Mon Jun 27 2016 - 00:33:36 CDT
Without directly addressing your question, I would point out that CHARMM36, at least, was parametrized and validated using PME: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549273/ <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549273/>
So not including it will introduce other artifacts, which may or may not be larger than the ones you are potentially worried about.
> On Jun 17, 2016, at 10:25 AM, Benjamin Brown <benjamin.p.brown17_at_gmail.com> wrote:
> Dear users,
> I am setting up simulations of several proteins so that I can examine the dihedral angle distribution of a particular loop region of each of them at equilibrium. From my understanding there are certain circumstances in which PME may bias proteins toward stability, and overestimate the representation of certain stable states in a protein's native ensemble compared to experimentally obtained ensembles (the main paper that comes to mind is the Weber et al. 2000 paper).
> My question is whether this behavior is primarily observed with respect to highly charged protein termini, or if I should be concerned that my loop dihedral distributions will also be biased. Would it be more accurate for my purposes to use a method other than PME?
> Thanks very much for the assistance,
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