Setting up aMD simulation of a membrane protein

From: Raul Araya (
Date: Fri Apr 01 2011 - 09:05:32 CDT

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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