[gmx-users] Protein-membrane system

[Itamar Kass]

Dear Aldo,

It is totally OK to see water molecules within the bilayer, both in 
simulations and real life. If I am not totally wrong, 3000 water 
molecule per lipids per second are being transferred across the bilayer 
without any protein involvement.

If your system is stable, the lipids density profile seems OK as well as 
its the thickness, you are fine.

Cheers,
Itamar.

On 17/02/11 5:48 AM, Justin A. Lemkul wrote:
>
> Aldo Segura wrote:
>> Dear gmx-users,
>>
>> I completed a MD (10 ns) of my protein-membrane system. When I 
>> perform a visual inspection (VMD) of md_0_1.gro file I observed a few 
>> water molecules within the bilayer. In previous steps (e.g. 
>> equilibration) this was not observed. Could be expected such behavior?
>
> Membrane protein systems take a long time (tens of ns or maybe more) 
> to equilibrate, so some water may drift in and out during the initial 
> few ns as voids in the lipids open and close.  Nothing to worry about, 
> unless for some reason they persist out past the expected 
> equilibration time.
>
> -Justin
>
>>
>> Best regards,
>>
>>
>> *//*
>>
>> */============================== =========
>> Aldo Segura-Cabrera
>> Laboratorio de Bioinformática
>> Centro de Biotecnología Genómica
>> Instituto Politécnico Nacional
>> Blvd. Del Maestro esquina Elías Piña, 88710
>> Reynosa, Tamaulipas, México.
>> (899)9243627 ext. 87747
>> e-mail: asegurac at ipn.mx <mailto:asegurac at ipn.mx>; 
>> aldosegura at gmail.com <mailto:aldosegura at gmail.com>
>> ============================== ===========/*
>>
>>
>>
>>
>

-- 


"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
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| Monash University,
| Victoria 3800
| Australia
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| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at monash.edu
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