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: [email protected] <mailto:[email protected]>;
[email protected] <mailto:[email protected]>
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| Postdoctoral Research Fellow
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