[gmx-users] freeze groups log file runaway

David van der Spoel spoel at xray.bmc.uu.se
Wed Jan 4 09:22:24 CET 2006

David Mobley wrote:
> Dear all,
> I've just started trying to use freezegroups to freeze a protein I've 
> been running MD on. As far as I can tell, according to the manual, 
> freezegroups = Protein should work even with pressure coupling 
> (Berendsen); the frozen groups should just be left unscaled by the 
> thermostat. Therefore, I thought it would at least be worth trying 
> having my protein frozen during constant pressure equilibration with 
> Berendsen.
> However, my log file (whenever I have pressure regulation) rapidly fills 
> up with the following:
> Correcting invalid box:
> old box (3x3):
>    old box[    0]={-9.99426e+21,  0.00000e+00, -0.00000e+00}
>    old box[    1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}
>    old box[    2]={-4.99713e+21,  3.07191e+28, -7.06701e+21}
> new box (3x3):
>    new box[    0]={-9.99426e+21,  0.00000e+00, -0.00000e+00}
>    new box[    1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}
>    new box[    2]={-4.99713e+21,  3.07191e+28, -7.06701e+21}
> The log file quickly runs away to several GB and I killed the job to 
> prevent overfilling my disk. Does this mean that freeze groups actually 
> do *not* work properly with pressure control? Or have I done something 
> wrong? I can submit a bugzilla if necessary.
If you have tried weaker coupling (e.g. tau_p = 2 ps) and it still 
happens then please do file a bugzilla.

> Thanks,
> David
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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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