There is no way to control for this when you solvate the box. After you solvate the box, you must do a short NVT simulation to allow the solvent to distribute evenly into any such gaps. After that, you should do a short NPT simulation to get the density right. Also, are you sure you need such a large box?
Chris Thiebaut
Graduate Student
Purdue University
----- Original Message -----
From: "Vytautas Rakeviius" <vytautas1987.yahoo.com>
To: amber.ambermd.org
Sent: Wednesday, April 9, 2014 8:39:12 AM
Subject: [AMBER] I make box with solvatebox complex TIP3PBOX 15.0 and unfilled gap remains near wall
I make box in xleap with command:
solvatebox complex TIP3PBOX 15.0
and unfilled gap remains near wall. I can see it in edit window.
I want my box fully filled with water. How can I avoid that gap?
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Received on Wed Apr 09 2014 - 10:30:03 PDT
