[gmx-users] [Fwd: Genbox doubt]

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 23 14:44:14 CET 2005

-------- 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 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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