Chris, is that for freeze groups or position restraints? On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale < chris.ne...@mail.utoronto.ca> wrote:
> No need to rename... just make an .ndx group. > > -- original message -- > > As I understand it, position restraints for an atom are set in the topology > file and applied to that atom in each of that species. In order to restrain > some but not all of the water I'd have to copy the topology of my water > model and add the restraints, then rename (and group together) the atoms I > want to freeze so that they're identified with the appropriate topology > file. Does this sound like it would work? Is there some other way that you > might do it? > > Thanks > > On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall <amarsh59 at uwo.ca> wrote: > > > 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 <bcostescu at > gmail.com>wrote: > > > >> On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall <amarsh59 at 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 at 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-request at 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 > > > > > > > -- > Alex Marshall > M.Sc. > 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 > -- Alex Marshall M.Sc. 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