Jianguo Li wrote:
Hi,
"3000 water molecule per lipids per second" corresponds to 0.000384
water molecules transferred across the membrane per nano second (assume
the system contains 128 lipids). It seems water translocation should not
be observed in a simulation of 10 ns, but I am not sure. And I only find
one reference paper(Biophysical Journal, Volume 96, 2009, pg4493–4501)
about the water translocation across the membrane, in which a asymmetric
membrane is used.
I also have similar observations for my protein-membrane system. I
observed 10~15 times water translocation arosss the membrane during 100
ns simulation when my protein adsorbed on the membrane. I am wondering
these water translocation is normal in all-atom simulations or they are
due to the protein-induced membrane deformation?
Sounds like a job for a proper control. If you see the same translocation in a
pure bilayer under the same conditions, then it's not likely to be related to
the presence of your protein, but rather an intrinsic feature of the model membrane.
-Justin
Any comment is highly appreciated, thank you!
best regards,
Jianguo
------------------------------------------------------------------------
*From:* Itamar Kass <itamar.k...@monash.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Thursday, 17 February 2011 07:20:19
*Subject:* Re: [gmx-users] Protein-membrane system
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: asegu...@ipn.mx <mailto:asegu...@ipn.mx>
<mailto:asegu...@ipn.mx <mailto:asegu...@ipn.mx>>; aldoseg...@gmail.com
<mailto:aldoseg...@gmail.com> <mailto:aldoseg...@gmail.com
<mailto:aldoseg...@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
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu <mailto:itamar.k...@monash.edu>
============================================
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========================================
Justin A. Lemkul
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
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Virginia Tech
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