GBIS and hydrophobic solvation

From: Jérôme Hénin (
Date: Mon Oct 10 2011 - 07:24:50 CDT

Hi everyone,

I have just read the very interesting paper that describes how
Generalized Born Implicit Solvent was parallelized in NAMD.[1] A
well-known limitation of GBIS is that it does not describe hydrophobic
solvation or the hydrophobic effect in water. That effect is of course
pretty important for protein conformation, and completely central to
anything involving membranes. That's why some implementations of GBIS
are augmented with empirical nonpolar solvation terms (e.g. [2]),
which NAMD does not have so far [3], although it implements the method
of Onufriev et al. who did use such a term in their work [4].

Given these circumstances, what classes of problems is NAMD/GBIS
well-suited for?

Thanks for your input,


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