[gmx-users] Re: gmx-users Digest, Vol 13, Issue 73

[David]

On Tue, 2005-05-31 at 14:21 -0400, Jason de Joannis wrote:
> 
> > On Thu, 2005-05-26 at 11:51 -0400, Jason de Joannis wrote:
> > > I am running a rather intensive (106K atoms) lipid bilayer simulation
> > > with PME for 100 ns. Initially the time-to-completion estimate is
> > > about 16 days. However over the course of 9 days the estimate increases
> > > monotonically to 110 days. I have run quite a few simulations like this
> > > before on the same hardware, though usually with cutoffs.
> > Is it exploding?
> NO.
> >
> > In parallel?
> NO.

Hard to say, check energy and density anyway.
Which gromacs version? Is the machine out of memory?
Are there other jobs running (run top).
> >
> > >        /Jason
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> >
> 
> But in the log file there are constraint warnings for every entry like this:
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.007034  15884  15885   0.001293
>         After LINCS         0.000041   4706   4707   0.000005
> 
> /Jason
> 
-- 
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
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