[gmx-users] unusually long run required

David van der Spoel spoel at xray.bmc.uu.se
Thu Feb 3 08:12:19 CET 2005

On Thu, 2005-02-03 at 10:38 +0000, jaimin at iitb.ac.in wrote:
> Dear Dr. Spoel:
> Regards.
> I wrote after going through the manual. For novices like me, it needs to
> be more descriptive. That is why I needed a small pointer from your or
> anyone's side so that I can go ahead.
> If I remove the solvent molecules manually from the .gro file generated
> after grompp, then the mdrun says it will complete the job on Feb 9th
> 2005. Although that is encouraging, I still need to know if there is
> some trick that would allow me to complete it in a few hours or one day.
Check whether you simulation uses any SSE (in the md.log file).
You didn't say what kind of machine you are running on. Anyway on a
regular P4 this should finish in minutes.

Please put further questions on the mailing list.

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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