AMBER Archive (2005)

Subject: AMBER: ptraj: determining solvent/ion densities

From: Joseph W.Toporowski (jtoporowski_at_chem.ucsb.edu)
Date: Thu Mar 17 2005 - 19:40:38 CST

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,
Joe

email: jtoporowski_at_chem.ucsb.edu
phone: x7158

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