[gmx-users] genion

[Christian Burisch]

Tamas Horvath wrote:

Hi all,

> Of course I can, but the only way to do that is to capture the pdb2gmx or
> grompp output as it seems...

it is also in the itp/top-File!

grep qtot protein.itp | tail -n 1

and then proceed with awk or perl or something like that.
Perhaps you should not only neutralise the system, but rather create a 
physiological ion concentration (which you can calculate of course 
from the system charge and the number of SOL molecules).

HTH

Christian