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

From: Giacomo Fiorin (
Date: Wed Jan 04 2017 - 08:24:18 CST

Hi Giota, it's very unlikely that you'll get decent conformational sampling
in the gel phase, so I would suggest sampling only temperatures above the

Note also that there are probably large free energy barriers between the
states of the system, depending on the hydrophobicity of the peptide. Just
raising the temperature may not be enough to cover them, and the membrane
may break apart before then.

You are probably better off running independent replicas, each prepared
from a different structure and compare their results.


On Tue, Jan 3, 2017 at 7:38 PM, Panagiota Kyriakou <> wrote:

> 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

Giacomo Fiorin
Associate Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
Philadelphia, PA 19122-1801
Phone: +1-215-204-4213 <(215)%20204-4213>
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*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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