[gmx-users] problem with genion

[gurpreet singh]

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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