[gmx-users] alkane-aqueous interfacial simulations

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 26 21:41:30 CET 2005

Jayant James Jayasundar wrote:
> Dear gmx_users,
> I am simulating a protein in hexane-aqueous, octane-aqueous and 
> decane-aqueous interfaces to understand the relation between activity 
> and interface hydrophobicity. I built the C6 & C8 molecules by means of 
> PRODRG (decane’s coordinates are already in Gromacs). The protein was 
> solvated in an aqueous environment containing 5777 aqueous molecules. In 
> this box sufficient number of alkanes were added such that they form a 
> spherical interface.
> The results of my simulations conducted over 5ns showed an expected 
> conformational change in a particular mobile loop of the protein that 
> covers the active site. The deviates are in the order, hexane < octane < 
> Decane ( least in C6- aqueous interface, moderate in C8-aqueous 
> interface greatest in decane-aqueous interface in terms of deviation 
> measured in Angstroms also verified by essential dynamics).
> Question
> Would Gromacs differentiate between a C6, C8, C10 based on their back 
> bone lengths so as to identify which is more hydrophobic interface.?

Yes, the solubility of C6 will be larger than C8 and C10. However, do 
not expect very good quantitative results. Check a recent paper by Villa 
& Mark about solubility of amino acids in hexan and water.

> Thanks
> Jayant
> Jayasundar Jayant James
> Research scholar
> Centre for Biotechnology,Anna University,
> Chennai - 600 025.INDIA .Ph 2350772(Office)
> www.chick.com/reading/tracts/0096/0096_01.asp)
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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