[AMBER] Cpptraj - Density Action Command Units

From: An Ta <anta.mymail.mines.edu>
Date: Thu, 9 Jan 2020 14:11:53 -0700

Dear AMBER users,

I have been looking into density profiles of a biphasic box primarily
composed of water and dodecane. Specifically, analyses were performed on
these solvent residues w.r.t. the z-axis. From my understanding, the
density values for the mass density command are in amu/A^3. But I was not
able to find anything that explicitly states this. Can anyone help confirm
or correct me if I am wrong?

Going off the basis that mass density is reported in amu/A^3, the
conversion to kg/m^3 is by a factor of x1660. However, this conversion
gives me values that are exceedingly high from what is expected. For
example, the "bulk area" or maximum of the density profile for water should
be ~1000kg/m^3. But the converted maximum values that I calculated are off
by a magnitude of 1000. Is there something that I may be missing or not
accounting for when converting the units of the reported values?

P.S. I have attached my results for my water mass density as well as
relevant input scripts. Please keep in mind that there are some acid in the
water and, thus, the density may be slightly off from the 1000kg/m^3 but I
am sure that it should not differ by x1000. Thank you for all of your
considerations and advisement.

*An T. Ta *
Department of Chemistry | Ph.D. Candidate
Coolbaugh Hall | Room 118
Golden, CO 80401

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Received on Thu Jan 09 2020 - 13:30:02 PST
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