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

reich at mpikg.mpg.de reich at mpikg.mpg.de
Mon Jan 28 18:42:44 CET 2008

Hi Berk,

thanks for your advice! I will try what you suggested and report back when
I have got the results.


>> Date: Mon, 28 Jan 2008 15:29:28 +0100
>> From: reich at mpikg.mpg.de
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure coupling
>> 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
>> 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
>> 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
> 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.

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