From: Arun Krishnan (krishnan_at_ttck.keio.ac.jp)
Date: Fri Nov 09 2007 - 01:24:36 CST
Dear All,
This might be a very simple question so please bear with me. How do I find
the density of water in the water box?
I found this answer in the archives:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/2330.html
in which it says: "I*f you used periodic boundary condition for a cubic
water box, the
density will remain constant and all you need to do is to determine the
total number of water molecules (the pdb will tell you that), multiply it
by the molecular mass of water, and then divide it by the volume of the
box to get the density in g/L.*"
Ok.. I got the number of water molecules from the pdb. Multiplied it by 18
(molecular mass of water). How do I get the volume of the box?
I think it is from the xsc file right? Do the a_x, b_y and c_z signify the
dimensions of the x,y and z dimensions of the water box in nm?
Would appreciate it if someone could kindly explain this.
Thanks,
Arun
-- *********************************************** Arun Krishnan, Ph.D, Assistant Professor, Institute for Advanced Biosciences, Keio University, Center Building, Tsuruoka, Yamagata 997-0035 Japan Phone: +81 (0)235-29-0824 Email: krishnan_at_ttck.keio.ac.jp URL: http://www.iab.keio.ac.jp/~krishnan **********************************************
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