[gmx-users] Problem with membrane simulation

[Neda Rafiee]

Thanks Mark! it worked...

----- Original Message -----
From: "Mark Abraham" <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Sent: Tuesday, February 7, 2017 7:20:28 PM
Subject: Re: [gmx-users] Problem with membrane simulation

Hi,

You can fill your box before you concatenate.

Mark

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

> Dear GMX-USERS,
> 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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