[gmx-users] Protein-membrane system

[Justin A. Lemkul]

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>
> ============================== ===========/*
> 
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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