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

Berk Hess gmx3 at hotmail.com
Thu Mar 27 16:18:08 CET 2008


I am also starting to wonder now if you might have other problems.
Have you checked if there aren't very strong volume fluctuations?

Could you mail your mdp pressure coupling parameters?


> Date: Thu, 27 Mar 2008 15:16:39 +0100
> From: reich at mpikg.mpg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
> 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.
> Best
> Luther
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