[gmx-users] a question about position restraint time for long alkyl chain molecules

[Justin A. Lemkul]

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 <jalemkul at vt.edu 
> <mailto:jalemkul at 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

========================================