[gmx-users] Freeze group atoms changing position

Justin Lemkul jalemkul at vt.edu
Thu Oct 25 03:22:21 CEST 2012

On 10/24/12 3:17 PM, Alex Marshall wrote:
> Hi all,
> I'm simulating a system of two reservoirs connected by a carbon nanotube.
> The reservoir wall atoms and carbon nanotube atoms are held in place using
> freeze groups at all times. I'm currently equilibrating the reservoirs
> separately by also freezing the water inside the nanotube, but after 20 ns
> two of the frozen water molecules have jumped outside of the nanotube into
> a supposedly inaccessible region. What could cause this? Should I be
> worried?

I would be.  Frozen groups aren't supposed to move at all.  Verify that the 
problematic water molecules are indeed contained within whatever frozen group(s) 
you have assigned in the .mdp file.  Otherwise, there's no immediate 
explanation, especially since other frozen atoms are staying frozen.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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