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

[Jason de Joannis]

> 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.
>
> >        /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

-- 
Jason de Joannis, Ph.D.
Emory University
1515 Pierce Dr, Atlanta, GA 30329
Phone: (404) 712-2983
Email: jdejoan at emory.edu
http://userwww.service.emory.edu/~jdejoan