[AMBER] Meaning of the term "pre-equilibrated" waters

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Sun, 21 Oct 2012 12:54:10 -0400

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)


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

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Received on Sun Oct 21 2012 - 10:00:03 PDT
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