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

[XUEMING TANG]

Got it (cool :)), Thank you!!!
Best!
Xueming

On Wed, Jun 8, 2011 at 1:15 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ========================================
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