[gmx-users] How to delete bad water molecules

David Mobley dmobley at gmail.com
Fri Nov 16 18:06:35 CET 2007


> I don't know the answer to the exact question that you have posed, but
> I instead suggest that getting rid of that water molecule is not a
> good idea. You should rather minimize your system. While minimizing,
> be sure to include
> define=-DFLEXIBLE
> in your .mdp file

Just out of curiosity, why do you think minimization should be done
with flexible water? I've gone the opposite direction and only
minimize with steepest descents since that's the only minimization
algorithm in gromacs that will work with constraints on hbonds, which
is how I run my dynamics, and I want to be minimizing on the same
potential energy landscape in which I'm running dynamics. That seemed
important. I'm curious why your strategy is different.


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