AMBER Archive (2006)

Subject: Re: AMBER: Density calculation

From: David A. Case (
Date: Mon Oct 16 2006 - 17:26:49 CDT

On Mon, Oct 16, 2006, Jianhui wrote:
> For NPT simulation, you will find DENSITY for the whole cell in the mdout
> file. Instead of the total density for the whole system, I want to know the
> density for one cluster part (for example the folded protein cluster). Is
> there a command in AMBER can finish this job? If not, how can I do this?

I don't know of any Amber command that would do this. Basically, you would
have to compute the volume of your protein cluster (maybe a Voronoi volume?),
then do a standard mass/volume calculation to get the density.


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