[gmx-users] "Correcting invalid box"

[David van der Spoel]

On Thu, 2004-01-08 at 04:02, Malcolm Gillies wrote:
> I'm running gromacs-3.2.0beta1.
> 
> The following message is appearing in md.log sporadically:
> 
> Correcting invalid box:
> old box (3x3):
>    old box[    0]={ 7.43601e+00,  0.00000e+00,  0.00000e+00}
>    old box[    1]={ 0.00000e+00,  7.43601e+00,  0.00000e+00}
>    old box[    2]={ 3.71886e+00,  3.71886e+00,  5.25805e+00}
> new box (3x3):
>    new box[    0]={ 7.43601e+00,  0.00000e+00,  0.00000e+00}
>    new box[    1]={ 0.00000e+00,  7.43601e+00,  0.00000e+00}
>    new box[    2]={ 3.71886e+00, -3.71715e+00,  5.25805e+00}
> 
> What does this mean? Should I be alarmed?
No, at least I don't think so, maybe Berk can comment? Due to pressure
coupling the box vectors have been modified, however, the length of the
box[ZZ] vector after coupling is slightly longer than the others, due to
numerical inaccuracy. This is corrected by this routine. What do your
original box vectors look like?

> 
> The simulation is being done with isotropic Parrinello-Rahman pressure
> coupling, in a dodecahedron box.
> 
> cheers,
> 
> Malcolm
> --
> Malcolm Gillies <Malcolm.B.Gillies at anu.edu.au>
> Postdoctoral Fellow, Computational Proteomics and Therapy Design Group,
> John Curtin School of Medical Research, Australian National University
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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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