Steven - I would use a simple harmonic bond.
Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 5:12 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > Thank you for this. And also I wish to attach a chain to my nanotube so they > will be both able to move together. Is that a matter of distance restraints > between nanotube atom and first atom of my chain or again - LINCS? Both > chain and nanotube are made of the same type of 8 type of atoms. Please, > advise. > > Steven > > > On Thu, Sep 26, 2013 at 3:19 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> > wrote: >> >> I am just curious why the system would explode without >> "periodic_molecules = yes". If the PBC procedure is applied before >> harmonic bond potential is calculated, than the opposite nanotube >> atoms should be (already) seen as neighboring. This looks the same as >> the solvent molecule, one atom of which crossed the box boundary. >> >> No? >> >> >> >> Dr. Vitaly V. Chaban >> >> >> On Thu, Sep 26, 2013 at 3:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> > >> > >> > On 9/26/13 8:39 AM, Steven Neumann wrote: >> >> >> >> Dear Gmx Users, >> >> >> >> I have my carbon nanotube and I wish to make it infinite in lenght. >> >> Which >> >> mdp options whall be used? pbc = xy and z is the infinite dimension? >> >> another issue: Would you apply bonds between carbon atoms within the >> >> nanotube or constraints using LINCS? Which of them is less >> >> computationally >> >> expensive for the run? >> >> >> > >> > Use "pbc = xyz" in conjunction with "periodic_molecules = yes" otherwise >> > the >> > topology gets messed up trying to form unreasonable bonds. The >> > periodic_molecules keyword in the .mdp allows for bonds to be maintained >> > over PBC. >> > >> > I remember a very old post somewhere in the archive that said one should >> > not >> > apply pressure coupling along the axis of the nanotube, due to some >> > difficulties with maintaining the bonded geometry, but since I have >> > never >> > done CNT simulations, take the fact that I'm just repeating what I've >> > heard >> > for what it's worth :) >> > >> > Constraints always come with the cost of communication, so I would >> > imagine >> > harmonic bonds are "less expensive." I really don't see constraints as >> > a >> > limiting factor for performance, though. >> > >> > -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 >> > >> > jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> > >> > ================================================== >> > -- >> > 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 >> -- >> 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 > > -- 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