[gmx-users] Skewed box using Parrinello-Rahman pressure coupling

reich at mpikg.mpg.de reich at mpikg.mpg.de
Thu Mar 27 15:16:39 CET 2008

Hi Berk,

I reran my simulations with the settings you suggested. Unfortunately most
of them crashed. In some of them I received the original error message:

Source code file: ns.c, line: 313

Fatal error:
Could not correct too skewed box

I did not, however, receive this message from all runs. In some cases
conformations were written out for a few steps shortly before the run
crashed, but the simulation process was killed before any error could be
written out. The log-files no proper ending in these cases. Is there any
way to get the error message before the simulation process is killed?

In one particular simulation the end of the log-file looked like this:

Correcting invalid box:
old box (3x3):
   old box[    0]={ 5.62033e+00,  0.00000e+00,  0.00000e+00}
   old box[    1]={ 2.79637e+00,  5.26160e+00,  0.00000e+00}
   old box[    2]={-2.81298e+00, -3.13776e-03,  4.54280e+00}
new box (3x3):
   new box[    0]={ 5.62033e+00,  0.00000e+00,  0.00000e+00}
   new box[    1]={ 2.79637e+00,  5.26160e+00,  0.00000e+00}
   new box[    2]={ 2.80735e+00, -3.13776e-03,  4.54280e+00}

t = 34154.008 ps: Water molecule starting at atom 1615 can not be settled.
Check for bad cont

I am not sure whether there is another problem with this simulation
causing the crash. But since the crash occurred directly after the
correction of the box I thought I should report this as well.



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