[gmx-users] Neutralizing

[Parham Jabbarzadeh (Department of Biomedical Science)]

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.topuniversities.com/universities/universiti-putra-malaysia-upm>
Malaysia

*​======​===================*Publication
<http://www.ncbi.nlm.nih.gov/pubmed/?term=Parham+Jabbarzadeh+Kaboli>:::
Featured
Publication
<http://www.sciencedirect.com/science/article/pii/S1043661815000833> :::
Website <http://www.parhamacademy.com/news.php> ::: FaceBook
<https://www.facebook.com/pkaboli/>


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.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.