[gmx-users] Hydrophobic interaction analysis

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 11 11:33:05 CET 2016

On 11/11/16 03:53, Mijiddorj Batsaikhan wrote:
> Dear gmx users,
> I simulated several peptide's folding. I would like to know the effects of
> hydrophobic interaction for the folding. How can I make analysis and know
> the effect of hydrophobic interaction?
> Is it possible to assess the hydrophobic interaction using short range Van
> der  Waals force?
Hydrophobic interactions do not exist. There is however, a hydrophobic 
effect, see, e.g.


What you can attempt is to compute enthalpy and entropy (but only if you 
have explicit water):
> Best regards,
> Mijiddorj

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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