[gmx-users] Killing mdrun based on execution time

[Samuel Coulbourn Flores 花山]

Hi Guys,

Is it possible to have mdrun die if it's still running after a  
specified amount of processor time?  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

Thanks

Sam