[gmx-users] Hydrophobic interaction analysis

[David van der Spoel]

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.

http://pubs.acs.org/doi/abs/10.1021/jp015514e
http://www.nature.com/nature/journal/v437/n7059/abs/nature04162.html

What you can attempt is to compute enthalpy and entropy (but only if you 
have explicit water):
http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.96.238102
>
> 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