[gmx-users] Skewed box using Parrinello-Rahman pressure coupling
gmx3 at hotmail.com
Wed Feb 13 17:05:41 CET 2008
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 BOX_MARGIN,
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 src/gmxlib/pbc.c.
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 coupling
> 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 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.
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