[gmx-users] Killing mdrun based on execution time

[Mark Abraham]

Samuel Coulbourn Flores 花山 wrote:
> Hi Guys,
> 
> Is it possible to have mdrun die if it's still running after a specified 
> amount of processor time?

Not within GROMACS.

>  I have an automatically initiated job that 
> sometimes hangs.  Alternatively, is there a way to have it give up upon 
> encountering a LINCS warning?  It seems to hang after getting one of these:
> 
> Step 1639, time 3.278 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 411690860544.000000 (between atoms 2093 and 2097) rms 
> 22468395008.000000
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, co

That means you haven't prepared your system well enough, equilibrated 
well enough, or similar. You should work on fixing the cause, not the 
symptoms. See 
http://wiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings

Mark