Hi Justin<br><br>Sorry I did not explain clearly. I apply position restraint to the head group of surfactant molecules and let all others (solvents and tail of surfactants) run freely. I am concerning about how long I should restraint the head group of surfactant molecules. If only concerning the solvent molecules, 10ps is enough for water to relax. But if concern the tail of the surfactant molecules, how to calculate the time of restraint (100ps, 500ps...). I guess 500ps position restraint will be enough? Is there any problem if I restraint the head group of surfactant micelle too long?<br>
<br>Thank you and have a nice day :P<br><br>Best!<br>Xueming <br><br><div class="gmail_quote">On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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XUEMING TANG wrote:<br>
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Hi there<br>
<br>
I put a SDS Spherical micelle in solution and want to apply position restraint before mdrun. Here I have a question: For macromolecules like micelles, should the position restraint apply to not only the water molecules (and ions) but also to the surfactant molecules in the micelle? If it is also for the surfactant molecules, how to calculate the position restraint time in this case. <br>
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Why would you restrain the solvent? That basically prevents equilibration from happening. Then, if you restrain the solvent and surfactant, you truly accomplish nothing.<br>
<br>
Likely the best course of action is to restrain the surfactant molecules, while allowing everything else to move freely. Then, remove all restraints and equilibrate a while longer.<br>
<br>
-Justin<br>
<br>
-- <br>
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<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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