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

XUEMING TANG yujan2007 at gmail.com
Wed Jun 8 19:12:11 CEST 2011


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?

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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110608/464787dc/attachment.html>


More information about the gromacs.org_gmx-users mailing list