[gmx-users] LINCS again
David van der Spoel
spoel at xray.bmc.uu.se
Fri Jun 11 11:49:37 CEST 2004
On Fri, 2004-06-11 at 03:44, F Jiang wrote:
> On Wed, 2004-06-09 at 03:15, F Jiang wrote:
> > Dear gmx-users,
> > Thanks for the previous replies. The b__topb__ command shows the CPU
> > ~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 b__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 b__lincs_iter? In any
> > I would think LINCS should abort instead of running for too long.
> avoid using constraints with minimization.
> Sorry David, I didn’t use constraints with minimization. I meant to
> say I got LINCS warnings when running mdrun_pr and it sometimes ran
> for a very long time. After increasing lincs_order, mdrun_pr seemed to
> be ok. And mdrun_md will run. Whether I’m doing meaningful things is
> another question, my starting structures have many bad geometries.
you could also try using shake, or even normal bonds using the
equilibration phase, but do check temperatures and energies.
> Thanks again---Fan
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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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