RE: [gmx-users] Specify run time
Thanks loads! That helps loads! Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Mark Abraham [mark.abra...@anu.edu.au] Sent: 20 May 2011 10:34 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Specify run time On 20/05/11, 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? GROMACS writes results progressively, so either choose a number of steps that will be suitable, or use mdrun -maxh. Then use the checkpoint to restart, per the restart instructions on the webpage Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Specify run time
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 p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | === -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Specify run time
On 20/05/11, Natalie Stephenson
wrote:
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> Hi All,
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> 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?
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GROMACS writes results progressively, so either choose a number of steps that
will be suitable, or use mdrun -maxh. Then use the checkpoint to restart, per
the restart instructions on the webpage
Mark
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--
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