[gmx-users] "Correcting invalid box"

[Malcolm Gillies]

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?

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