Thanks a lot. You the bond as a distance between atoms? I wish to avoid bonds as they are not necessary...just position restraint. What would be the force constant? I tried 1000 once without bonds and my atoms were moving a bit...
Steven On Thu, Oct 10, 2013 at 2:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/10/13 9:21 AM, Steven Neumann wrote: > >> How about applying position restarints with a strong force constant? What >> is less computationally expensive: position restrained, freezing the whole >> molecule? The nanotube should be rigid... Shall I place the edged of the >> > > You shouldn't see any real performance gain or loss by applying either > restraints or freezing. > > > tube on the box edge as well and use pbc=xyz and periodic molecules = yes? >> >> > The box size needs to be (length of tube) + (bond length). If you place > the carbon atoms at the box edge, they overlap and the system blows up. > > > -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@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
