[gmx-users] Re: periodic molecule

Valentina valentina.erastova at durham.ac.uk
Wed Sep 18 14:07:46 CEST 2013

Thank you!

Yep, they seem to be wanting to bond to the O's within the cell, while they
are meant to bond across the PBC.

I am not sure how periodic_molecule = yes part functions. I don't seem to
get difference if I turn it on or off when I do Energy minimisation. Do you
have some examples that work, so I can compare to them? Are there some
threshold distances, that they rely upon? I really wouldn't like to have to
make the a bigger basic cell - too much topology assigning. 


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