AMBER Archive (2007)

Subject: AMBER: Truncated Octahedron box volume

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Sun Jul 22 2007 - 21:52:16 CDT

Dear All,

I am trying to calculate the volume of a particular snapshot by using the
box info printed at the last part of an .rst file. The volume of a
truncated octahedron is defined as

V = 11.3137085 * a^3

where a is the edge length.

In my .rst file, the last line is

51.9046302 51.9046302 51.9046302 109.4712190 109.4712190 109.4712190

and assuming the edge length is 51.9046302, the volume becomes as

V = 1582061.232393538433

When I use process_mdout.perl, and check out the summary.VOLUME file,
amber calculates the volume as

V = 107645.7776

I will appreciate if someone can tell me where I am doing wrong. Thanks. 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemistry      -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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