[gmx-users] Freeze group atoms changing position

[Bogdan Costescu]

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