[gmx-users] Place water away from existing atoms

Justin A. Lemkul jalemkul at vt.edu
Thu May 17 17:46:05 CEST 2012

On 5/17/12 11:16 AM, Steven Neumann wrote:
> Thank you. Is it possible that this is caused by the trapped molecules inside my
> tube? My tube ends are on the box edges so water cannot migrate outside the tube
> where are the other water molecules.

I take it that your tube is finite, not infinite?  I guess I'm confused at this 
point - there are water molecules inside the tube?  I thought the whole point 
was to not have water inside.

In any case, if your tube is finite with the ends at the box edges, you likely 
have clashes between tube atoms that cause the water to start kicking around. 
If you have a small number of molecules within the tube, then yes, they can 
become unstable in isolation.  This commonly occurs with voids in simulation boxes.



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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