[gmx-users] Question about analysing micelle structure

Ran Friedman r.friedman at bioc.uzh.ch
Fri Jan 25 14:40:21 CET 2008

Dear Alif,

In principle, all of your suggestions are possible. It may be that the
FF parameters are not modelled correctly, that the equilibration takes a
long time (do you observe any changes in shape during the 10ns
simulations?) or that something isn't right. Also, do you mimic the
experiment in terms of solvent and temperature? This may also make a
change. Try to search the literature for similar models. In addition,
try to calculate as many physical properties of the system as you can to
compare with experiments. This may give you a hint of what's going wrong
and how to fix it.

Good luck,

Alif M Latif wrote:
> Greetings GROMACS users and developers,
> I've been studying about the structure of a nanoemulsion of palm-oil
> and surfactant in water. Many simulations have been performed. My
> first objective is to replicate the experimental work done and then
> study the structural properties. I'm using GROMACS (its free,
> flexible, and fast!!). Simulations produced convincing results; at low
> composition=no micelle formation, 30% lipid=cylindrical micelle,
> higher % = two phase (bilayer-like).
> Its all going the right way until I changed the surfactant with higher
> HLB value which, (Israelachivli, 2005) theoretically tend to produce
> spherical micelle. I'm still getting cylindrical, I did simulation
> with only surfactant and water, (assuming the long-chained oil
> structure was the culprit). Both surfactants (higher and lower HLV
> value) still produced cylindrical micelle. My questions are:
> --Is this got anything to do with my parameters? (in .mdp file?) 
> --Misconcept? Do i need to prepare spherical micelle as the initial
> structure and then run MD? right now my initial molecules scattered
> aroung the   simulation box randomly.
> --Can longer simulation time produce spherical? (I've already did 10 ns)
> I'm pretty confident about the composition of oil and surfactant
> (experimental data). Could anyone suggest better way? Valid way to do
> this.. I'm short of experience and no one had done this before
> right here. Sorry for the long mail. I need help. Thank you very much
> for reading. Advices, comments and suggestions are greatly welcomed.
> Thanks again,
> Alif (Msc. Student)
> Chemistry Department,
> Faculty of Science, Universiti Putra Malaysia.
> Serdang, Selangor, Malaysia.

Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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