[gmx-users] mdp option periodic molecules

[Johannes Hermann]

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