[gmx-users] neutralizing membrane protein in lipid bilayer +water

ram bio rmbio861 at gmail.com
Tue Sep 29 15:30:55 CEST 2009

Dear Gromacs users,

I have a modelled protein whose net charge is +12.69, and I would like to
ionize the protein to make it neutral using genion command, but in genion
command we can add a specific number of postive or negative charged ions
which for my case would not completely neutralize the system and i learnt
from Justin tutorial that we can even neutralize it using -conc and -neutral
options in conjugation. As I am running a membrane-protein simulation, I
would like to know the command which I am using is correct or not.

genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+ -nname
CL- -nn 12 -neutral

If my command is wrong Please suggest the right one as In future i have to
conjugate SOL and CL- ions to create a special index file.


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