[gmx-users] Freeze group atoms changing position

Alex Marshall amarsh59 at uwo.ca
Wed Oct 24 21:17:05 CEST 2012

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

Alex Marshall

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