Re: [gmx-users] mdrun -nsteps
Alright, thanks! Am 17.02.2015 13:48, schrieb Mark Abraham: Hi, The second call to mdrun will run 1 steps if it can. Whether that is a continuation or not depends what checkpoint mdrun finds, etc. gmx mdrun -h says -nsteps Run this number of steps, overrides .mdp option This is true, from the point of view of the next MD simulation part, which is what mdrun does. That this part is just one piece of a bigger picture isn't something mdrun needs to help you manage, I think. Using the word append would be ambiguous, because gmx mdrun -append refers to running some number of steps and concatenating the output files (or not, with -noappend). Continue doesn't fully work either, because it implies the existence of a previous simulation part. The main alternative would be defining -nsteps as do this total number of steps, starting from the checkpoint (if any). This isn't very usable unless you know for sure what is in your checkpoint. The current meaning for -nsteps means that it is easy to write a job submission script e.g. for 2 hours doing 50,000 more steps - which is awkward otherwise. Cheers, Mark On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The second mdrun runs until 15000 steps, not 1 steps. Is this intended? If yes, the option description is somewhat misleading. Cheers Sabine -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun -nsteps
Hi Sabine, The option says to run for so many steps, which is exactly what happens. So in total, you run for 15000 steps, but that one run you said to run for 1, did run for exactly 1. Cheers, Tsjerk On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The second mdrun runs until 15000 steps, not 1 steps. Is this intended? If yes, the option description is somewhat misleading. Cheers Sabine -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun -nsteps
Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The second mdrun runs until 15000 steps, not 1 steps. Is this intended? If yes, the option description is somewhat misleading. Cheers Sabine -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun -nsteps
Hi, The second call to mdrun will run 1 steps if it can. Whether that is a continuation or not depends what checkpoint mdrun finds, etc. gmx mdrun -h says -nsteps Run this number of steps, overrides .mdp option This is true, from the point of view of the next MD simulation part, which is what mdrun does. That this part is just one piece of a bigger picture isn't something mdrun needs to help you manage, I think. Using the word append would be ambiguous, because gmx mdrun -append refers to running some number of steps and concatenating the output files (or not, with -noappend). Continue doesn't fully work either, because it implies the existence of a previous simulation part. The main alternative would be defining -nsteps as do this total number of steps, starting from the checkpoint (if any). This isn't very usable unless you know for sure what is in your checkpoint. The current meaning for -nsteps means that it is easy to write a job submission script e.g. for 2 hours doing 50,000 more steps - which is awkward otherwise. Cheers, Mark On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser sabine.reis...@kit.edu wrote: Hi, just to be sure: is it intended, that the -nsteps option in mdrun (which is a great feature in general!) actually appends the given number of steps rather than overriding the mdp option? This is what I do: - grompp with mdp file with 5000 steps - mdrun - mdrun -nsteps 1 steps The second mdrun runs until 15000 steps, not 1 steps. Is this intended? If yes, the option description is somewhat misleading. Cheers Sabine -- Dipl. Phys. Sabine Reißer Karlsruhe Institute of Technology (KIT) Institute of Physical Chemistry Phone +49 (0) 721 / 608-45070 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
