RE: AMBER: What does a crash mean while running a md simulation?

From: Ross Walker <>
Date: Mon, 24 Jan 2005 11:19:48 -0800

Dear Shuli,

> I`m running a long md simulation.So I divided the simulation into
> several jobs.
> One of the jobs suddenly stoped for something wrong.And the next job
> started automaticly according to the .rst file produced before the
> crash. No error or warning information appears in the log
> file.And the
> consequent job seems fine now.
> What may be the reason for the crash ?Should I rerun the crashed job?

This could be due to anything, without more information it is hard to tell.
Are you running in a queuing environment (PBS?). If yes have you hit the
time limit for your job? PBS will often kill a job with no error message if
you exceed the maximum wallclock or cputime allowed. You might also faulty
hardware, this could cause a job to crash with no error message.

Secondly, if you ran the job just backgrounded in a shell, without nohup,
closing that shell will kill the job.

You also redirect standard error to a file so that the error message is not


Sander -O -i mdin -o mdout -p prmtop -c inpcrd >& logfile

As for the new job starting immediately from the crashed job this is fine,
except for the fact that it will have started from an earlier time in the
simulation than you were expecting. Make sure you are aware of this and
adjust your interpretation of the results as necessary.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Jan 24 2005 - 19:53:01 PST
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