[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Justin,
> 
> 
> 2011/11/11 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     If the bilayer is splitting across periodic boundaries (I'm assuming
>     that's what you mean by "pb"), then it's more likely that you placed
>     the components of your system in an inconvenient way than it is that
>     something is actually wrong.
> 
> 
> Bilayer has moved on Z-dimension in periodic box.  That is actually 
> what's  happend :)
> http://i1209.photobucket.com/albums/cc394/own11/vmdscene.gif
> 

How large of a void exists between your lipids and water prior to starting the 
simulation?  I'm almost certain that you built the unit cell incorrectly - there 
should never be that much free space.

> 
> By the way I'ts intresting that Gmembed has removed 6 lipids in 
> comparison to the inflateglo ( althought I've done all things in 
> accordance to the KALP tutorial because my protein is the same). 
> 

Different algorithms, different results.  Nothing odd about that to me.

-Justin

-- 
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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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