[gmx-users] mdp option periodic molecules

[Johannes Hermann]

Perfect, Thanks!

On 06.03.20 09:00, Christian Blau wrote:
> Hi Johannnes,
>
>
> That is correct.
>
> Another confirmation of what you already suspect is found in the 
> manual in
>
> http://manual.gromacs.org/documentation/current/reference-manual/topologies/molecule-definition.html 
> <http://manual.gromacs.org/documentation/2020/reference-manual/topologies/molecule-definition.html> 
>
>
> "Molecules can be made infinitely long by connecting to themselves 
> over periodic boundaries. When such periodic molecules are present, an 
> option in the mdp file needs to be set to tell GROMACS not to attempt 
> to make molecules that are broken over periodic boundaries whole again."
>
>
> Best,
>
> Christian
>
> On 2020-03-06 08:52, Johannes Hermann wrote:
>> Dear all,
>>
>> could you please confirm if I understood the periodic molecules entry 
>> (I already browsed through the manual and mailing list):
>>
>> I need "periodic molecules = yes", if a molecule interacts=connects 
>> to itself via covalent bonds over the periodic boundary.
>>
>> I do NOT need "periodic molecules = yes", if a molecule interacts via 
>> non-covalent interactions to itself via PBs. In this case "periodic 
>> molecules = no" is the right choice.
>>
>> Is that right?
>>
>> Thanks in advance!
>>
>> All the best
>>
>> Johannes
>>
>>
>>
-- 
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*Technische Universität München*
*Johannes Hermann, M.Sc.*
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