[gmx-users] Re: gmx-users Digest, Vol 13, Issue 73
spoel at xray.bmc.uu.se
Tue May 31 21:58:03 CEST 2005
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?
> > In parallel?
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
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
More information about the gromacs.org_gmx-users