[gmx-users] Question about analysing micelle structure

[Chris Neale]

>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?) 

Yes it relates to your cutoffs, etc. because everything relates to your cutoffs, etc. but assuming that you took proper such conditions from the papers that developed the forcefield that you are using then no I don't think that you should not change your parameters just because you don't see what you expect.

>--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.

Sounds like a good setup to me, unless your computational resources are highly restricted.

>--Can longer simulation time produce spherical? (I've already did 10 ns)

I highly doubt that 10ns is sufficient. Aim for 125ns.

>I'm pretty confident about the composition of oil and surfactant (experimental data). 

By composition do you mean concentration? 30% lipid by weight is a massive concentration. It actually doesn't surprise me that you don't get micelles. Do they really get micelles at this concentration experimentally? Monoolein 40% w/w in water gives cubic-Pn3m phase experimentally. In fact, addition of detergent pushes it toward La phase (Liu and Caffrey J. Struct Biol. 150 (2005) 23-40.)

>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.