[gmx-users] Specify run time

Peter C. Lai pcl at uab.edu
Fri May 20 11:41:30 CEST 2011

On 2011-05-20 04:13:55AM -0500, Natalie Stephenson wrote:
> Hi All,
> I was just wondering if anyone knew whether it was possible to tell Gromacs to run for a few hours, dump all the intermediate results and then exit.  I was hoping to be able to use the checkpoint function to run the simulation for a bit, checkpoint it, exit then restart.  Is this possible?

Yes, when you send the master process SIGTERM (^C), it should dump a check
point file for you (in version 4+). You can also specify -cpt n to 
have it write a cpt file every n minutes (default is 15min I think). So you 
could just have your system scheduler kill your master mdrun process after 
some hours then restart.
See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
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