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Dear Alif,<br>
<br>
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.<br>
<br>
Good luck,<br>
Ran.<br>
<br>
Alif M Latif wrote:
<blockquote cite="mid280370.44352.qm@web53712.mail.re2.yahoo.com"
type="cite">
<style type="text/css"><!-- DIV {margin:0px;} --></style>
<div
style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div>Greetings GROMACS users and developers,</div>
<div> </div>
<div>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). </div>
<div> </div>
<div>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: </div>
<div> </div>
<div>--Is this got anything to do with my parameters? (in .mdp file?) </div>
<div> </div>
<div>--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.</div>
<div> </div>
<div>--Can longer simulation time produce spherical? (I've already
did 10 ns)</div>
<div> </div>
<div>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.</div>
<div> </div>
<div>Thanks again,</div>
<div> </div>
<div>Alif (Msc. Student)</div>
<div>Chemistry Department,</div>
<div>Faculty of Science, Universiti Putra Malaysia.</div>
<div>Serdang, Selangor, Malaysia.</div>
<div> </div>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
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