From: Benjamin Brown (benjamin.p.brown17_at_gmail.com)
Date: Fri Jun 17 2016 - 10:25:44 CDT
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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