[gmx-users] problem with genion

[gurpreet singh]

Thanks Tsjerk
I  referred  the mail about  the broken molecules but there the problem is i
think somewhat different. in that case broken molecules are coming becasue
of the PBC . since PBC is being used that is why some part of the molecule
is coming from the other side of box and its looking as if protein is broken


but in my case i think the situation is different, first of all i have not
still started using the PBC in the simulation and my full molecule (broken
molecule) is right in the center of the box. moreover  i am getting this
problem before starting any simulation. till i did some simulation in vaccum
before adding ions , it went fine there and then while shifting to the water
simulation i added ions and right after adding the ions my molecule is
getting broken.


Thanks
With Regards
Gurpreet

7/16/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> 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
> _______________________________________________
> 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!
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