[gmx-users] more CPU usage and LINCS

[F Jiang]

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.

 

Thanks very much.

Fan 

 

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