[gmx-users] more CPU usage and LINCS
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 9 09:28:11 CEST 2004
On Wed, 2004-06-09 at 03:15, F Jiang wrote:
> Dear gmx-users,
> Thanks for the previous replies. The ‘top’ command shows the CPU is
> ~0% user ~100% system. I get this problem when mdrun_pr goes on
> forever (>2000mins CPU) and when there are many LINCS warnings and
> huge bond deviations. I tried ‘lincs_order=50’ with l-bfgs and then
> mdrun_pr (with a few initial steps generating LINCS warnings) and
> mdrun_md could run. Should I also increase ‘lincs_iter’ ? In any case,
> I would think LINCS should abort instead of running for too long.
avoid using constraints with minimization.
> Thanks very much.
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
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