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

[reich at mpikg.mpg.de]

Hi Berk,

the change of parameter worked! My simulation finished without crashing.


Thanks for your help

Luther


>> Dear Gromacs-users,
>>
>> I have been performing simulations with cubic and octahedron-shaped
>> boxes
>> using Parrinello-Rahman pressure coupling. After some time I get the
>> error
>> message "Could not correct too skewed box" and the simulations crash.
>> I set the parameters for the coupling as listed below:
>>
>> pcoupltype               = isotropic
>> tau_p                    = 5.0
>> compressibility          = 5e-5
>> ref_p                    = 1.0
>>
>>
>> I have never encountered the same problems when using Berendsen pressure
>> coupling so I suppose I must have made a bad choice for some parameter
>> for
>> the Parrinello-Rahman barostat. I tried to equilibrate my system using a
>> Berendsen barostat before switching to Parrinello-Rahman for 1ns (and
>> tau_p=1.0) but this didn´t help. Do you have any clue about where the
>> problem originates from?
>>
>>
>> Best
>>
>> Luther
>
> I guess this is a rounding issue in the box checking/correcting routines.
> Could you change BOX_MARGIN in include/pbc.h from 0.5001 to 0.5005,
> recompile gmxlib, mdlib and mdrun and see if the problem still occurs?
> Please report back, so we can fix this for 3.3.3.
>
> Berk.