[gmx-users] Freeze group atoms changing position

[Alex Marshall]

Chris, is that for freeze groups or position restraints?

On Wed, Oct 31, 2012 at 3:22 PM, Christopher Neale <
chris.neale at 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
> >> --
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> >
> >
> >
> > --
> > 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
> --
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-- 
Alex Marshall
M.Sc.
Department of Applied Mathematics
The University of Western Ontario