Justin Lemkul wrote > On 9/18/13 8:07 AM, Valentina wrote: >> 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 > > I have never used periodic molecules, except when toying around with some > CNTs > for my own curiosity. I suspect the problem you're seeing arises from the > bonded atoms being closer within the unit cell than they are across PBC, > so the > minimum distance is what is trying to be satisfied. > > > > Nope, thats not the case. > Across pbc it's 2.06A while across the cell it's 7.89A (see the attached > pic, where in bold are the atoms whitin the cell and small are the > periodic representation it should bond to) <http://gromacs.5086.x6.nabble.com/file/n5011279/Screen_Shot_2013-09-18_at_13.30.23.png> > > How far apart are the atoms > across PBC, and how long is the assigned bond supposed to be? I have seen > other > cases posted to the list wherein the periodic_molecules function breaks > down > simply because of bad starting geometry. > > >> threshold distances, that they rely upon? I really wouldn't like to have >> to >> make the a bigger basic cell - too much topology assigning. >> > > A bigger unit cell won't help. In fact, it would probably make things > worse. > > Agree, thank you! > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201
> jalemkul@.umaryland > | (410) 706-7441 > > ================================================== > -- > gmx-users mailing list > gmx-users@ > 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-request@ > . > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- View this message in context: http://gromacs.5086.x6.nabble.com/periodic-molecule-tp5011270p5011279.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
