[gmx-users] Freeze group atoms changing position

Alex Marshall amarsh59 at uwo.ca
Fri Oct 26 23:18:22 CEST 2012

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

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