[gmx-users] connectivity issue

Fitsiou, Eleni e.fitsiou at lancaster.ac.uk
Fri Dec 14 13:38:39 CET 2018

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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