[gmx-users] Manually aborting a simulation

Mark Abraham Mark.Abraham at anu.edu.au
Fri May 20 00:48:18 CEST 2011

On 20/05/2011 3:45 AM, Justin A. Lemkul wrote:
> Andrew DeYoung wrote:
>> Hi,
>> I have started a lengthy equilibration run, and I just realized that 
>> I have
>> one of my parameters set incorrectly in my mdp file.  Is there any 
>> way that
>> I can manually abort the run?
>> I am using Gromacs 4.5.4 with parallel simulation with MPI and the 
>> command:
>> mpirun  -machinefile cp -np 8 mdrun -s nvt-pr.tpr -o nvt-pr.trr -c 
>> water.pdb
>> -e nvt-pr.edr -g nvt-pr.log &
> Use 'ps' to locate the process ID and kill it in the terminal.

The above command will only still be running if its terminal is still 
alive, and from that terminal you can use "jobs", which will give you a 
small number associated with all such running processes. Now "kill %n" 
will kill it, or "fg %n" to bring it to the foreground so that Ctrl-C 
will kill it.


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