[gmx-developers] Re: Re:Re:Re:Re:Re: Energy Minimization

Igor Leontyev ileontyev at ucdavis.edu
Thu Jun 25 09:49:14 CEST 2009

>(Berk Hess)
> The first issue is a technical one.
> In general one can have conflicting demands, one can freeze atoms
> as well as require constraints. The question is what to do with frozen
> atoms between which there are constraints that are not at the correct 
> length
> in the initial structure. I chose to use masses for frozen atoms that
> are 10^24
> higher then normal. In that way constraints between frozen atoms will
> be correct, whereas frozen atoms should move 10^24 less than non-frozen
> atoms connected by constraints. Therefore I would expect that your
> water oxgyens should move very little.
> By how much did they move?

Frozen TIP3P oxygens,  whose hydrogens have been optimized, are shifted up 
to 0.8 A. 

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