Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip.
Bogdan: I don't think I'm using constraints other than freeze groups. I wasn't using energy group exclusions though. I tried running the simulation from the same initial configuration with newly-defined energy groups CNT_GRA_WAL_IN and OUT, the first for the frozen atoms and the second for the free atoms. The list of exclusions reads: energygrp_excl = CNT_GRA_WAL_IN CNT_GRA_WAL_IN Long story short, I'm roughly 15 ns into the simulation and the same two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu <bcoste...@gmail.com>wrote: > On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amars...@uwo.ca> wrote: > > 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. > > Are you using some kind of constraints ? Are you using energy group > exclusions to avoid interactions between frozen atoms ? If you search > the manual for "frozen" you'll find some warnings and recommendations. > > Cheers, > Bogdan > -- > 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 > -- 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
