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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Sep 13 06:03:28 CEST 2006

>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

>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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