[gmx-users] problem with system neutralization

Pawan Kumar pawan.chinari at gmail.com
Fri May 22 12:24:01 CEST 2009


Greetings from Pawan.
-np is a parameter used to add the nmber of positive ions.
when u have -4 negative charge u should give -np 4.
-np with -pname will be more appropriate.
see through this website for the proper usage of genion options.

On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga <smeliga at gmail.com> wrote:

> Dear all,
> As the on-screen output of grompp says, my system has non-zero total charge
> = -4.000
> Thus, I'm trying to neutralize the system using genion with this command
> line:
> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top
> -neutral
> The problem is that the on-screen output says:
> "No ions to add and no potential to calculate"
> as the system was already neutral, I guess.
> I then tryied with the command line:
> genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p 4AKEallHsol_pre.top
> -neutral -np 50 -g
> Ions are added to the SOL group but the total charge remains -4, as the log
> file says.
> Do you know the reason?
> Thanks a lot,
> Stefano
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