[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Fri Nov 11 19:47:13 CET 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list