AMBER Archive (2004)

Subject: AMBER: DENSITY in constant pressure MD

From: nlxc (nlxc2000_at_yahoo.com)
Date: Tue Jun 15 2004 - 13:17:41 CDT

Hi,
 
I am running MD for a complex of protein and ligand under constant pressure condition with ibelly=1 (only 20 A around liagnd can move). I use "solvatecap complex WATBOX216 { x y z} 20" to add 20 A water around the center of ligand. I have used the above setting to try several different protein-ligand systems. After about 400ps MD, the density of some systems are equilibrated at around 0.8, some are around 0.5, some are around 1.2. My question is why there is so much variation among different systems. Is it normal or something wrong with my setting? Any suggestions are highly appreciated. Thanks in advance.
 
Nan

                
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