Amber Users and Developers,
I use a truncated octahedral box in my calculations and I'm hoping someone can help me understand the information listed for the volume of the box (unit cell) in sander output. I've looked through the Amber and AmberTools user guides and have searched the archives, but have been unable to locate any useful
answer.
It seems clear that the volume listed in the output is calculated from the dimensions and angles given in the last line of the .rst file as if it were a triclinic cell (e.g, 62.195... 62.195... 62.195... 109.471... 109.471... and 109.471... gives a volume of 185242 which is consistent with a volume listed as 185241, allowing for a 1-step difference in these data). The total mass of molecules in the box is 2.5852 x 10^-19 g. However, the density listed in the output, 1.0242 is not consistent with (total mass)/(listed volume). Thus, my question is how is the volume of the triclinic cell related to that of the truncated octahedral box?
I would greatly appreciate any help. Thanks!
Robert Hopkins, Ph.D.
Professor Emeritus, Chemistry and Biophysics
University of Houston - Clear Lake
e-mail: hopkins.uhcl.edu
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Received on Sat Dec 04 2010 - 10:00:04 PST
