GBIS and hydrophobic term, in replay to Jerome and David discussion

From: Branko (
Date: Sun Oct 23 2011 - 09:36:17 CDT

Jerome, David,

After your discussion on hydrophobic term in GBIS, I compare my
simulations using expl. and impl. EtOH with one small flexible molecule
(as a part of ongoing study). Indeed free-energy surface, obtained by
ABF (Jerome topic) looks different, providing that more conformation
have a lower energy, but shape of the surfaces is a same. More
importantly global minima are very comparable. Conformation sampling is
also very, very similar (I use one distance, previously chosen as a
colvar, which in reasonable way describe conformational change). Plot of
~ 40 conformational clusters from exp. vs. same no of clusters obtained
by impl. solvation give r = 0.98. Molecule under simulation can be
described as amphyphylic, having one hydrofobic end and other with two
carboxylates, so during simulation hydrophobic interactions could be
considered as non-negligible.
So looks that by implicit solvation one can obtain something 'lower
energy content' in vast majority of samples, but structurally results
are very similar.


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