[gmx-users] Neutralizing

Parham Jabbarzadeh (Department of Biomedical Science) pjabbarzadeh at gmail.com
Tue Mar 8 08:44:21 CET 2016

Dear Sir

Use this command:

gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -neutral

In this case, you don't need ​the number of ions​.

Kind Regards

Parham J. K.

​PhD candidate - Lecturer in drug discovery
Faculty of Medicine and Health SciencesUniversity Putra Malaysia

<http://www.sciencedirect.com/science/article/pii/S1043661815000833> :::
Website <http://www.parhamacademy.com/news.php> ::: FaceBook

On Tue, Mar 8, 2016 at 3:32 PM, mohammad r <mohammad.r0325 at yahoo.com> wrote:

> Hi everybody, I’ve generated a water-peptide system, now I want to
> neutralize it. Is adding adequate number of ions sufficient for
> neutralizing process or I should do QM/MM simulation for the this
> process? Thank you, Mohammad.
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