Waters pre-equilibrated in a box, which is superimposed on the solute
with overlapping waters subtracted, leaving voids. Allow for shrinkage.
On 10/21/2012 9:54 AM, Sajeewa Pemasinghe wrote:
> Hi all,
>
> I have a protein around the center of which I am adding a waterCap
>
> So when I say
>
> solvateCap a TIP3PBOX a.324.NH1 50.0 2.5 It adds 5735 waters (50.0
> Angstrom is a bigger value than the maximum radius of the protein)
>
> with
>
> solvateCap a TIP3PBOX a.324.NH1 55.0 2.5 It adds 9954 waters.
>
> When I calculate the density of the water in the outer shell of 5 Angstrom
> width (which has 9954-5735=4219 waters) I get a density of 0.728 gcc. I
> thought I would get a value much closer to 1.000 gcc as it says in the
> tutorials that xleap adds "pre-equilibrated" waters. So I wanted to know
> what I am missing. What exactly does it mean by "pre-equilibrated"?.
> Doesn't it refer to water with density close to 1.000 gcc?
>
> Thank you
>
> Sajeewa
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Received on Sun Oct 21 2012 - 18:00:03 PDT
