[gmx-users] Protein-membrane system
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 17 12:46:33 CET 2011
Jianguo Li wrote:
> "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.
> Any comment is highly appreciated, thank you!
> best regards,
> *From:* Itamar Kass <itamar.kass at monash.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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.
> 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
> > -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>
> <mailto:asegurac at ipn.mx <mailto:asegurac at ipn.mx>>; aldosegura at gmail.com
> <mailto:aldosegura at gmail.com> <mailto: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
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu <mailto:Itamar.Kass at monash.edu>
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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