And also ... my tube has 1200 atoms and I wish to apply [ exclusions ] - is there any gmx tool to exclude interactions within the given molecule so 1 with all 1200, 2 with all 1200...etc... 1200 with all 1200?
Steven On Thu, Oct 10, 2013 at 2:34 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > 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