Hi there,
In addition to setting -pq to 2 as Justin said, you can set -conc to a
very low value such as 0.00001 for neutralizing the system.
One more thing... genion apparently uses the box volume when
determining how many ions are necessary for getting a given ionic strength.
However, depending of your system size and shape and box type the volume
of the protein may be considerable. Maybe the number of water molecules,
instead of the box volume, is a better criterion for determining the number
of ions to be added.
best regards,
Leandro
2012/9/9 Matthias Ernst <[email protected]>
> Hi,
>
> I just encountered (another) strange thing with genion.
> I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
> forcefield amber99sb), so I expected half of the system charge (-52) to be
> added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26
> which would be needed for neutralization. The same holds for Zn or Ca ions,
> which also are divalent in ions.itp
>
> Could it be that the routines of genion to determine the number of ions
> are not working properly? I mean, the -neutral option also does work only
> if the -conc flag is also there and provides a value > 0.0 (which in fact
> is not what I want when I just want do neutralize my system by adding
> ions...)
>
> Does anyone of you also had similar problems?
>
> Thank you,
> Matthias
> --
> gmx-users mailing list [email protected]
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
> posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to [email protected].
> * Can't post? Read
> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
