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

[reich at mpikg.mpg.de]

Hi Berk,

my volume fluctuations are relative small. For the largest and smallest
system respectively that I have been simulating the statistics are:

       Average        RMSD       Fluct.
      207.7 nm^3    0.699 nm^3  0.698 nm^3
       75.1 nm^3    0.431 nm^3  0.432 nm^3

My pressure coupling parameters are:

; Pressure coupling
Pcoupl                   = Parrinello-Rahman
pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 5.0
compressibility          = 5e-5
ref_p                    = 1.0


Best

Luther

> Hi,
>
> 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?
>
> Berk.
>
>
>> 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