[gmx-users] Killing mdrun based on execution time

[David van der Spoel]

Mark Abraham wrote:
> 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.

It will be in release 4.

> 
>>  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

Agreed.

> 
> Mark
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se