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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
