Re: [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 
 



"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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*Johannes Hermann, M.Sc.*
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Re: [gmx-users] mdp option periodic molecules

[Christian Blau]

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 



"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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