[gmx-users] Neutralizing

mohammad r mohammad.r0325 at yahoo.com
Tue Mar 8 09:59:18 CET 2016

Thank you Parham 
You mean that it is not necessary to do QM/MM simulation?

    On Tuesday, March 8, 2016 11:13 AM, Parham Jabbarzadeh (Department of Biomedical Science) <pjabbarzadeh at gmail.com> wrote:

 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 MalaysiaMalaysia
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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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