[gmx-users] Re: Simulation problem with extended membrane system!

liu xin zgxjlx at gmail.com
Mon Sep 18 10:03:59 CEST 2006

Thanks Chris, I really appreciate your help!
I've got my extended membrane system regarding your note, and now I'm
testing it with my GPCR. I am still not very familiar with the script, I
think it will take some time to learn.

Thanks again!

On 9/13/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> >If I solvate my GPCR into the DPPC128 system using genbox, there are only
> >about 50 lipids left, which I think are too few, so I want a larger
> starting
> >structure.
> >According to your note, when I did step 3, loaded my DPPC183 system to
> VMD,
> >I found the edges lined up poorly, there is are gaps between two periodic
> >cells. I also try other system like DPPC200, DPPC150, but only the
> original
> >dppc128 system, I've equilibrated it for 2ns,  have no  gap between two
> >periodic cells.
> >So, I will try another starting structure, like POPC, DMPC or your POPE.
> But
> >I still can't figure out why there are gaps when using genbox to extend
> the
> >DPPC system.
> It's because any overlap causes an entire lipid to be removed.
> If you don't want to equilibrate, try exactly doubling your system size in
> x and
> y. That should work perfectly.
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