[gmx-users] Fwd: Questions for the forum

[Matilde Viegas]

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