[gmx-users] freeze groups log file runaway

David Mobley dmobley at gmail.com
Wed Jan 4 00:21:06 CET 2006

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.

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