[gmx-users] Skewed box using Parrinello-Rahman pressure coupling
gmx3 at hotmail.com
Mon Jan 28 16:08:08 CET 2008
> 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 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?
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.
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