Thanks a lot. I will use position restraints then with a strong force constant, no bonds and place the edge atoms within half of distance between them from the box edge. Is that correct?
Steven On Thu, Oct 10, 2013 at 2:56 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/10/13 9:54 AM, Steven Neumann wrote: > >> Thank you. I do not have any explicit solvent in my system. I included the >> solvent in nonbonded parameters so not even implicit. >> >> > Well, presumably you have other things in the system, otherwise you're > simulating an inert tube of non-interacting atoms, which I doubt is useful > for anything. Basically what I'm trying to say is freezegrps is listed as > a non-equilibrium option for a reason - it does not correspond to physical > reality and can seriously perturb your system in bad ways. It's really > only useful for equilibrating problematic systems, and nothing else IMHO. > > > -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
