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. Thanks, V -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011277.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
