[gmx-users] problem with genion

[Tsjerk Wassenaar]

Hi Gurpreet,

You probably performed energy minimization without a box, without PBC.
Then you generated a box using editconf. That's where the PBC comes
in. With genbox you fill the thing with solvent, and running grompp
then will provide you a run input file, which is set up to be used for
a simulation. That means, that molecules are shifted such that they
are properly arranged with respect to the reference box, which does
not need to correspond with what you think is the proper arrangement
(i.e. all components together more or less in the center of the box).

Exercise:

Take the run input file you use as input for genion and convert it to
.gro/.pdb for viewing (using editconf -f -o). Compare it with the
structure you used as input to grompp. Be sure also to visualize the
box and work out the shifts over the lattice (box) vectors.

Tsjerk


On 7/16/07, gurpreet singh <gps.iitm at gmail.com> wrote:
> 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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-- 
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