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
