[gmx-users] connectivity issue

[Fitsiou, Eleni]

Hello,

Just double check during the production phase too.You are welcome ! Παρακαλώ  
> On 14 Dec 2018, at 12:45, antonia vyrkou <avyrkou at gmail.com> wrote:
> 
> 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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