[gmx-users] Duplicate lipid bilayer, simulate protein and remove extra lipid bilayer

[Mark Abraham]

Hi,

There are many bilayer building webservers on the net, Google around and
pick what fits your needs.

Mark

On Thu, Oct 12, 2017 at 10:45 AM Du, Yu <duyu at sioc.ac.cn> wrote:

> Dear GMX Users,
>
>
> My question is 512-lipid bilayer is too big. How can I resize it and the
> cooresponding box size?
>
>
> I duplicated the 128-lipid bilayer using
> $gmx_mpi genconf -f lipid128.gro -o lipid_new.gro -nbox 2 2 1
>
>
> But the new 512-lipid bilayer is so large, I want to remove the some
> lipids according to the x and y coordinate.
>
>
> I know the parameter -nbox uses integers. But is there any easy way to
> fulfill the function like `gmx_mpi genconf -f lipid128.gro -o lipid_new.gro
> -nbox 1.5 1.5 1`?
>
>
> --
> Du, Yu
> PhD Student,
> Shanghai Institute of Organic Chemistry
> 345 Ling Ling Rd., Shanghai, China.
> Zip: 200032, Tel: (86) 021 5492 5275
> --
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