[gmx-users] Problem with membrane simulation

Mark Abraham mark.j.abraham at gmail.com
Tue Feb 7 16:50:43 CET 2017


You can fill your box before you concatenate.


On Tue, 7 Feb 2017 16:42 Neda Rafiee <nerafiee at ipm.ir> wrote:

> I have a major problem with building my system which contains two parallel
> bilayers. If I use different servers such as CHARMM-GUI or ATB or any
> other, I will have gro and top file and I can concatenate two bilayers into
> one simulation box. But when I fill the box with water (using $gmx editconf
> ... and $gmx solvate ...), I will have water all over the box, and it is
> not desirable. I want to have water moleculed just above and under
> bilayers. On the other hand, if I use Packmol software, I will get my
> desirable coordinate file, but I cannot produce .top and .gro with pdb2gmx
> according to what Lindahl suggest in this video:
> https://www.youtube.com/watch?v=nwMiqP4g1Zo
> Has anyone worked with Packmol for lipid bilayers?
> Thanks
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