[gmx-users] Skewed box using Parrinello-Rahman pressure coupling
reich at mpikg.mpg.de
reich at mpikg.mpg.de
Thu Feb 14 14:31:15 CET 2008
thanks again. I am not sure though whether I have understood what
modifications you have suggested. In src/gmxlib/pbc.c there are several
occurrences of BOX_MARGIN, some with and some without a factor of two.
Should each occurrence be multiplied by two (so those that have the factor
already are left as they are and all others get multiplied)? Could you
post the lines 71 to 76 of src/gmxlib/pbc.c with the right corrections so
that I can be sure to implement them correctly?
Also, should I leave the value for BOX_MARGIN in include/pbc.h at 0.5005
or change it back to 0.5001 ?
> That good news.
> While looking at the code again just now,
> I realized what the actual problem is.
> The check before and after the box correction are both done with
> which can lead to the problem you observed when the last bit of the box
> is rounded in an unlucky fashion. So even with your change the problem
> could still occur.
> A real fix is adding a factor 2 (2*) in front of BOX_MARGIN in
> I have added this fix for the 3.3.3 release.
>> Date: Wed, 13 Feb 2008 16:37:55 +0100
>> From: reich at mpikg.mpg.de
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] Skewed box using Parrinello-Rahman pressure
>> Hi Berk,
>> the change of parameter worked! My simulation finished without crashing.
>> Thanks for your help
>> >> 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
>> >> 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
>> > 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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