How to perform REMD of a system a membrane-protein system?

From: Panagiota Kyriakou (kyria008_at_umn.edu)
Date: Tue Jan 03 2017 - 18:38:54 CST

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Hello NAMD community,

I wish to perform an all-atom REMD simulation of a membrane-protein system
(a 40-residue peptide). My membrane is a bilayer consisted of POPG and POPE
lipids and I want to explore temperatures above 300K (above their
gel-liquid transition temperature).
Does any of you have any suggestion/advice on how to treat the lipids?
Should I constrain them? Is there a maximum temperature that I should heat
my system?

Thank you in advance,
Giota

Panagiota Kyriakou
PhD Candidate in Chemical Engineering
Dept. of Chemical Engineering and Materials Science
University of Minnesota

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