[gmx-users] Place water away from existing atoms

Justin A. Lemkul jalemkul at vt.edu
Thu May 17 16:59:46 CEST 2012

On 5/17/12 10:38 AM, Steven Neumann wrote:
> Well, I am still getting the same error when I try to do minimization: "water
> molecule on atom X cannot be settled" - these water molecules are not close to
> the Tube surface. If I will remove them the same error will occur but on the
> other atoms. If I specified only vdwradii for my Tube atoms why in the bulk of
> water there are some overlaps? Can you please help?

The problem is not necessarily with the water molecule, but is more often 
indicative of some other instability in the system, such that forces are 
transmitted to that poor unsuspecting water molecule and it blows up.


It's hard to diagnose, so make sure you're EM step is very small and you save 
configurations frequently in order to diagnose what's happening.  It could be a 
problem with the .mdp file, topology, or perhaps some weird water overlap, but 
if that's the case, then genbox didn't do it, something else caused it.



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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