Re: Setting up aMD simulation of a membrane protein

From: Jeff Wereszczynski (
Date: Fri Apr 01 2011 - 11:00:23 CDT

Hi Raúl,

My two cents would be to try simulations of both the dihedral and dual
boost options and see how your system behaves.

I see your concern about boosting the dihedrals in the lipid, but I
don't think this is a bad thing, and I wouldn't worry about
restraining the lipid positions. If you have a solvated protein, one
of the advantages of dual-boost (relative to just dihedral aMD) is
that the diffusivity of the water increases, so the protein has an
easier time moving through the solvent. Analogously, if you boost the
dihedrals in the lipid environment that your protein is surrounded by
you may find that protein motions are enhanced since its easier to
push the lipids around. By contrast, if you did restrain the lipid
positions what you might find is that you are "freezing" the
environment around the protein and you could end up preventing the
protein motions you are hoping to see.

Hope that helps,


Jeff Wereszczynski
NIH Postdoctoral Fellow
University of California, San Diego
On Fri, Apr 1, 2011 at 7:05 AM, Raul Araya <> wrote:
> Dear NAMD users:
> I'm interested in using the aMD module of NAMD 2.8b1 for the study of
> possible conformational changes of a large trans-membrane protein. I
> want to know how must I confront this problem in terms of defining the
> aMD parameters.
> 1) Should I use the aMDd option, where only the dihedral angles
> present on the system will be boosted?? In that case, I must have in
> mind that the Lipid molecules in which the protein is embedded (POPC)
> also posses dihedrals, so the will be boosted as well as the protein.
> What could this produce? Should I worry about that? should I apply
> constraints to the carbon atoms of the lipids to prevent a not-normal
> behavior of the bi-layer? Or the value for the boosting factor should
> only consider the dihedral energy of the protein atoms and with that I
> will not see any exaggerated effect on the lipids?
> 2) On the other hand...maybe I should consider a boosting of the total system??
> Any help will be most appreciated....
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.

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