[gmx-users] Fwd: Questions for the forum

[Matilde Viegas]

I tried to downzise to 10 and yet the reduction was very little. I was just
trying t understand how can the difference between the same systems, using
either AMBER or GROMACS, can be of 1 million atoms...

2016-10-13 12:27 GMT+01:00 Dd H <ddhecnu at gmail.com>:

> You can reduce your box size to get a smaller system.
>
> On 13 October 2016 at 17:41, Matilde Viegas <matildefrviegas at 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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