Accelerated MD with membrane embedded proteins.

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Mon Mar 28 2011 - 13:45:36 CDT

Dear NAMD users:

I'm very happy with the addition of the aMD capabilities to NAMD 2.8.
Bur I have a question regarding aMD simulation of a protein embedded
in a POPC lipid bi-layer:

- As I understand DIHEDRALS will not only be defined for the protein
part of the system, and they will be considered also for the lipid
molecules. Considering that, It is advisable to perform an aMDd
simulation of such system aiming at enhance the conformational
sampling of the protein and search for interesting conformational
changes? What could be the effects of applying the boosted potential
to the lipid molecules in the system?

- With that in mind, what other possible method could be applied to
the system in order to look for conformational changes in the protein
with little knowledge of the possible conformational changes to
sample?

Thanks in advance.

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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