[gmx-users] Re: gmx-users Digest, Vol 13, Issue 73
Jason de Joannis
jdejoan at emory.edu
Tue May 31 20:21:21 CEST 2005
> 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?
> > /Jason
> 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 de Joannis, Ph.D.
1515 Pierce Dr, Atlanta, GA 30329
Phone: (404) 712-2983
Email: jdejoan at emory.edu
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