[gmx-users] Problem in equilibration for membrane system

[Itamar Kass]

hi Bing,

I advice you to look carefully on any clashes between POPC and the
protein. It might happen that one lipid was 'trapped' inside the
protein or more likely that atom water had trapped and that what crash
you system.

Cheers,
Itamar

---

 "In theory, there is no difference between theory and practice. But,
in practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at med.monash.edu.au
============================================

On Wed, Oct 7, 2009 at 9:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Bing Bing wrote:
>>
>> My protein complex was minimized initially before putting into the lipid.
>> POPC is also a preequilibrated structure from Tielemen website. I don't
>> quite understand on what you meant by "the protein is not happy with the
>> restraint". The system went well through out the nvt, npt with
>
> I think what Mark was getting as was if you're restraining some unusual or
> inappropriate geometry, you can get nasty results when you turn off
> restraints.  I don't know that this is the case in your situation.
>
>> restraint on protein.... Once it move to md production run ( which is
>> without restraint on protein), error occurred (range checking error). The
>> reason i'm using the version3.3.2 is because the forcefield i'm using at the
>> moment only support version3.3.2.  Is my problem cause by
>
> I don't understand this statement.  The force field you mentioned is most
> certainly supported in the newest version of Gromacs, in fact my tutorial
> was written for the version 4.0.x series.  Please also see the advanced
> troubleshooting page I provide; you may find some ideas there.
>
> Certainly, watch the trajectory and see where things are going wrong to
> deduce the nature of the issue.
>
> -Justin
>
>> bug of the older version? is there any bugfix fot this? please
>> help.
>>
>> regards,
>> Bing
>>
>>
>> On Wed, Oct 7, 2009 at 4:15 PM, Mark Abraham <Mark.Abraham at anu.edu.au
>> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>>    Bing Bing wrote:
>>
>>        Dear All,
>>        I'm running the protein complex with POPC system. NVT (100ps)
>>        and NPT (200ps) were done with restraint on the protein follow
>>        by 1000 ps of NPT without restraint on protein. The trajectory
>>        was checked in term of pressure, potential, area per lipid
>>        ....were checked and everything seems ok (potential almost
>>        plateu, area per lipid close to experimental value). I proceeded
>>        with md (similar to Justin's tutorial) for 1 ns. The simulation
>>        stop around 800ps with the range checking error.
>>
>>
>>    OK so look at the collective variables, and/or trajectory to find
>>    evidence of the problem. The most likely explanation is that your
>>    protein was unhappy in the restraints, of course. Perhaps you should
>>    try some vacuum EM before you embed it in the lipid, or some such.
>>
>>
>>        I'm using gromacs 3.3.2, with GROMOS9653a6 forcefield. I tired
>>        to be more gentle while releasing the restraint.Different
>>        stepwise of releasing the restraint during NPT were tried and
>>        followed by production MD, all the simulation stop or i shall
>>        said it crashed around ~800ps with the same error (range
>>        checking error). I'm out of idea what is the problem here.
>>        Please advice.
>>
>>
>>    Range checking is just one of many things that can be the first
>>    thing to break when there's an underlying systemic problem.
>>
>>    Also, unless you need scientific continuity, 3.3.2 is about 4 years
>>    old... 4.0.5 will be much faster!
>>
>>    Mark
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>>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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