XUEMING TANG wrote:
Hi Justin
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?
I doubt you can restrain anything too long. If all the relevant thermodynamic
observables have converged (T, P, energy, etc), then your restrained
equilibration is probably sufficient. Once you remove the restraints, you'll
have to assess some structural properties of the micelle to know if it is
equilibrated before collecting data. Maybe density, size, etc.
-Justin
Thank you and have a nice day :P
Best!
Xueming
On Wed, Jun 8, 2011 at 12:51 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
XUEMING TANG wrote:
Hi there
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.
Why would you restrain the solvent? That basically prevents
equilibration from happening. Then, if you restrain the solvent and
surfactant, you truly accomplish nothing.
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.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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