You can reduce your box size to get a smaller system.

On 13 October 2016 at 17:41, Matilde Viegas <matildefrvie...@gmail.com>
wrote:

> Hi,
>
> my name is Matilde. This is my first time using GROMACS. I'm switching from
> AMBER to GROMACS however I'm having some trouble reproducing my system:
>
> In AMBER, I'm working with a 5000 residues protein, a water box (TIP3) of
> 12A, roughly 1.5 million atoms total. I tried building the same system in
> GROMACS, cubic box, 12A, same protein, however I obtain a 2.5 million atoms
> system. Is there a way I can reduce the number of atoms?
>
> Thank you in advance,
> Matilde
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