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

[Justin A. Lemkul]

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

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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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