[gmx-users] The right way of killing Gromacs

[Berk Hess]

>From: kobi <kobi17 at gmx.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] The right way of killing Gromacs
>Date: Fri, 15 Sep 2006 11:33:27 +0200
>
>Hello,
>
>the runtime of our cluster is unfortunately limited. Before mdrun is 
>terminated a USR1 signal is
>send, but this doesn't cause mdrun to writeout the current frame. Therefore 
>most of the trajectory
>is lost. I'd like to write a skrip which converts the USR1 sinal to some 
>other signal. The question
>is, which signal would cause mdrun to write out all data and terminate it 
>afterwards?

mdrun -h explains it.
The USR1 signal is what you want, but it should NOT be sent to the master 
process
that spawned the others, and you want to send it in time, that is long 
enough
before the queue time ends so you can reach the next nstvout step.

Berk.