AMBER Archive (2006)

Subject: AMBER: Solvating a bilayer

From: Matthew Tessier (
Date: Fri Dec 15 2006 - 13:32:25 CST


I'm trying to solvate an equilibrated lipid bilayer and I wanted to know if
there was a method I could use to solvate above and below the bilayer
without getting waters placed inside the bilayer in areas that are large
enough to fit a water molecule (like around the edges). I've been able to
bypass this in un-equilibrated bilayers by using the following command:


solvateBox LIPID TP3 { 0 0 16 } 1.6


Upon heating, the gap between the waters and lipids collapses quickly and so
a 1.6 Angstrom buffer is corrected for during the early stages of the MD
simulation, but I would have to use a much larger buffer in the equilibrated
bilayer. Is there a way to prevent waters from being placed in a certain
region based on coordinates or some other method that could fix my problem?


-Matt Tessier

University of Georgia

CCRC - Woods Lab


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