[gmx-users] [Fwd: Genbox doubt]

[Alan Dodd]

The way I see it, genbox dumps in randomly oriented
waters until there's no more room, and if the box size
isn't just right, there's going to be thin gaps near
the edges where there isn't quite space to fit more
water in.  The larger the box, the more the rest of
the box damps this out and hides this effect.  If you
have NPT conditions (constant pressure) then I think
it should fix the density as soon as you run any MD,
but even if you run under constant volume I guess it's
less than a 1% error... there are bigger things to
worry about in MD.

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> -------- 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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