Thanks. I will place them then within the distance from the box edge = distance between atoms within the tube right? I can create bonds and use harmonic spring constant like for backbone protein atoms...but whats the point when they do not move anyway? I am using NVT.
Steven On Thu, Oct 10, 2013 at 2:37 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/10/13 9:34 AM, Steven Neumann 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... >> >> > If you don't have bonds, then there is no point using periodic_molecules. > Still, the point stands that you cannot place atoms at the box edge, > because they will overlap via PBC regardless of periodic_molecules. > > Using freezegrps causes artifacts, especially with pressure coupling, so > if you want to model the tubes as rigid, then the only real option that I > can think of is to simply increase the force constant for the restraints. > I don't particularly understand this approach, as people have done tons of > simulations of nanotubes with normal bonded geometry. > > > -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
