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

From: Jérôme Hénin (
Date: Sun Oct 23 2011 - 09:43:08 CDT

Hi Branko,

This is good news, but not very surprising since EtOH has weaker
self-interactions than water, hence a much smaller cavitation free
energy and "ethanolphobic effect".


On 23 October 2011 16:36, Branko <> wrote:
> 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.
> Branko

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