[gmx-users] removing a water molecule

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 28 08:44:43 CEST 2007

Ragothaman Yennamalli wrote:
> Dear all,
> I am running a MD simulation, which stops after 6ns
> run with an error saying:
> t = 6825.932 ps: Water molecule starting at atom 19637
> can not be settled.
> Check for bad contacts and/or reduce the
> timestep.Wrote pdb files with previous and current
> coordinates
> How does one proceed from here? Is removing the single
> water molecule a solution? In that case wouldn't there
> be a conflict between the number of atoms of previous
> trr file and the new one being made?

Yes, you can't continue from where you are. You should have a close look 
at what's been happening and see if there are any other problems. 
Probably you need a more gentle minimization-equilibration regime at the 


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