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

From: Panagiota Kyriakou (
Date: Mon Jan 09 2017 - 16:34:03 CST

Hi Giacomo,

Thank you for your response and your suggestion. It is very helpful!

Could you please explain to me how the hydrophobicity of the peptide
affects the free energy barriers of the system?

What do you think about Replica Exchange Solute Tempering (REST)? Do you
think it could work instead of classic REMD?
I recently read an article by Huang et al "Acceleration of Lateral
Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute
Tempering <>" where they
perform REST on a bilayer with Gromacs. However, I think that a similar
protocol can be followed with NAMD since I think there is an option for

Thank you,

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

On Wed, Jan 4, 2017 at 8:24 AM, Giacomo Fiorin <>

> 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 transition.
> 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.
> Giacomo
> 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>
> Scholar:
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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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