[gmx-users] problem with genion

[Tsjerk Wassenaar]

Gurpreet,

I didn't ask whether you used PBC, I suggested it was due to PBC.
Check the archives for "broken molecules" and such.

Tsjerk

On 7/16/07, gurpreet singh <gps.iitm at gmail.com> wrote:
> Thanks Tsjerk for you reply
> i did not get your point . i think you are asking me whether i used PBC or
> not , so i want to tell you that the .tpr file which i used for genion
> command was created without using PBC.
>
>  but will it make any difference ?
>
> Thanks
> With Regards
> Gurpreet
>
> On 7/16/07, Tsjerk Wassenaar <tsjerkw at gmail.com > wrote:
> >
> > Gurpreet,
> >
> > >  my system was going fine at that time but when i used the genion
> command to
> > > add ions , i found that my protein was broken into parts.
> > >  what could be the reason for this ?
> >
> > PBC?
> >
> > >  While running the genion it usually asked for the group into which we
> want
> > > to add the ions so i have checked with both the SOL group and OTH group
> > > seperatly , in both the cases ions were replacing the solvent molecules.
>  Is
> > > their any way by which we can add ions without replacing any solvent
> > > molecules ?
> >
> > No, there's no space to put them.
> > Well, you could try to squeeze them in here or there manually, and
> > perform energy minimization...
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623