AMBER Archive (2004)

Subject: Re: AMBER: DENSITY in constant pressure MD

From: David A. Case (
Date: Tue Jun 15 2004 - 17:50:57 CDT

On Tue, Jun 15, 2004, nlxc wrote:
> 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.

I am confused here. You can only run constant pressure MD for a periodic
system, but the "solvatecap" option does not create a periodic box. What is
the value of ntb that you are using? What version of Amber? I think we need
to know more about how you prepared the system, and what sorts of input
parameters you are using.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to