[gmx-users] freeze groups log file runaway

[David Mobley]

This didn't seem to solve the problem, so I've submitted a bugzilla. I can,
of course, run the constant pressure equilibration with position restraints
rather than freeze groups if necessary, but I would rather use freeze groups
for everything if possible, since I really don't want the protein to move at
all, ever, in what I'm doing. I just want to equilibrate at constant
pressure to bring the bath to the right pressure.

Thanks,
David

On 1/4/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> David Mobley wrote:
> > Dear all,
> >
> > I've just started trying to use freezegroups to freeze a protein I've
> > been running MD on. As far as I can tell, according to the manual,
> > freezegroups = Protein should work even with pressure coupling
> > (Berendsen); the frozen groups should just be left unscaled by the
> > thermostat. Therefore, I thought it would at least be worth trying
> > having my protein frozen during constant pressure equilibration with
> > Berendsen.
> >
> > However, my log file (whenever I have pressure regulation) rapidly fills
> > up with the following:
> >
> > Correcting invalid box:
> > old box (3x3):
> >    old box[    0]={-9.99426e+21,  0.00000e+00, -0.00000e+00}
> >    old box[    1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}
> >    old box[    2]={-4.99713e+21,  3.07191e+28, -7.06701e+21}
> > new box (3x3):
> >    new box[    0]={-9.99426e+21,  0.00000e+00, -0.00000e+00}
> >    new box[    1]={ 0.00000e+00, -9.99426e+21, -0.00000e+00}
> >    new box[    2]={-4.99713e+21,  3.07191e+28, -7.06701e+21}
> >
> > The log file quickly runs away to several GB and I killed the job to
> > prevent overfilling my disk. Does this mean that freeze groups actually
> > do *not* work properly with pressure control? Or have I done something
> > wrong? I can submit a bugzilla if necessary.
> If you have tried weaker coupling (e.g. tau_p = 2 ps) and it still
> happens then please do file a bugzilla.
>
> >
> > Thanks,
> > David
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060104/a3cf0d17/attachment.html>