[gmx-users] LINCS again

F Jiang jiangf at aphy.iphy.ac.cn
Fri Jun 11 03:44:02 CEST 2004

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 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 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 case,

> 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. 

Thanks again---Fan


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