[gmx-users] connectivity issue

[antonia vyrkou]

Hello Eleni,

Thank you for your reply. I actually thought about that possibility after I
posted my problem and since I've triple checked my input files I assume
that's what is going on.
Thanks again!
Ευχαριστώ!

Best regards, Antonia

On Fri, Dec 14, 2018 at 12:39 PM Fitsiou, Eleni <e.fitsiou at lancaster.ac.uk>
wrote:

> I think it is probably a visualisation issue ..If the bond is not in the
> topology, then you are fine. VMD for example uses a criterion based on the
> distance to show the bonds.
>
> Best, Eleni
> > On 14 Dec 2018, at 11:12, antonia vyrkou <avyrkou at gmail.com> wrote:
> >
> > Hello,
> >
> > I am a bit puzzled by the following problem
> >
> > After the energy minimization,  in one type of molecules, appear two
> bonds
> > that should not exist. If I visualize the pdb before the minimization
> > everything is normal. After the minimization this problem appears.
> > I checked the ffbonded.itp, the aminoacids.rtp, and the the .itp files,
> and
> > all connectivity is normal.
> >
> > Any ideas?
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