[gmx-users] [Fwd: Genbox doubt]

[David van der Spoel]

-------- Forwarded Message --------
From: Fernando Mattio <mattiofer at gmail.com>
To: gromacs at gromacs.org
Subject: Genbox doubt
Date: Wed, 23 Nov 2005 13:34:01 +0100

Dear gromacs users,

I have doubts about the genbox... For example, with the command genbox
-cs spc216.gro -o box2.gro -box 2 2 2 the volume of the box created is 8
nm³, Density = 796,495 g/L and 213 sol molecules were created.
If I try genbox -cs spc216.gro -o box5.gro -box 5 5 5 the volume of the
box created is 125 nm³, Density = 991,273 g/L and 4142 sol molecules
were created. 
With genbox -cs spc216.gro -o box12.gro -box 12 12 12 the volume of the
box created is 1728 nm³, Density = 999,375 g/L and 57727 sol molecules
were created. 

So, in all the cases I think that I have created a box only with solvent
on it... And in normal conditions the density of water is something
around 1000g/L. So I would like to understand how the genbox works, does
it try to reach this density of normal conditions??? And why the
difference of densities in the 3 cases, if I did almost the same thing
in the 3 situations?? If I want a density of 1000 g/L, how can I manage
the genbox in order to get it?

Thank you very much in advance and best regards,
Fernando Mattio
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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