[gmx-users] problem with system neutralization

[Stefano Meliga]

Thanks Pawan,

I added 4 positive ions as you suggested but the system total charge 
reported in genion.log is still -4!

Why?

Cheers,

Stefano


Pawan Kumar ha scritto:
> Hello,
>
> 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.
> http://www.gromacs.org/documentation/reference_3.3/online/genion.html
>
> Regards,
> Pawan
> On Fri, May 22, 2009 at 3:20 PM, Stefano Meliga <smeliga at gmail.com 
> <mailto: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
>     _______________________________________________
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php