AMBER: determining solvent/ion densities

From: Joseph W.Toporowski <>
Date: Mon, 14 Mar 2005 15:35:25 -0800

Dear Amber community,

I have recently generated grid files for solvent and ion density
distribution for a trajectory file using the "grid" function of PTRAJ,
and have used Midas to succesfully view the files.
My question involves the correlation between contour levels and true
density. How does one determine what each contour level refers to in
terms of atom density? Is there a function that would allow the
visualization of, for example, a specific number of ions per volume?

Thanks for any input on this matter.


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Received on Mon Mar 14 2005 - 23:53:01 PST
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