Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd starts counting at 0) and checked confout.gro to make sure the coordinates matched up. I only have one group for all frozen atoms in the system, and these guys are definitely in it.
On Wed, Oct 24, 2012 at 9:22 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/24/12 3:17 PM, Alex Marshall wrote: > >> Hi all, >> >> I'm simulating a system of two reservoirs connected by a carbon nanotube. >> The reservoir wall atoms and carbon nanotube atoms are held in place using >> freeze groups at all times. I'm currently equilibrating the reservoirs >> separately by also freezing the water inside the nanotube, but after 20 ns >> two of the frozen water molecules have jumped outside of the nanotube into >> a supposedly inaccessible region. What could cause this? Should I be >> worried? >> >> > I would be. Frozen groups aren't supposed to move at all. Verify that > the problematic water molecules are indeed contained within whatever frozen > group(s) you have assigned in the .mdp file. Otherwise, there's no > immediate explanation, especially since other frozen atoms are staying > frozen. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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> > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- 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
