Thanks Justin, and Tsjerk for the helpful comments. I think I can get away with a simple for-loop as Justin recommended.
Greg On Thu, Aug 25, 2011 at 4:14 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey : > > In scripts, like on the command line, processes wait for earlier > processes to finish, unless these are brought to the background using > the ampersand '&' at the end of the line. If you want to execute > something in the background in your script, to allow checking the > progress automatically, for instance, you can make sure some later > process does not start before the ones in the background finished by > using the command 'wait': > > mdrun -deffnm [...] & > wait > grompp [...] > mdrun -deffnm [...] & > wait > echo FINISHED > > Hope it helps, > > Tsjerk > > On Thu, Aug 25, 2011 at 9:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > > > Yongchul Chung wrote: > >> > >> Hello gmx-users, > >> > >> I am trying to run a sequence of energy minimizations for a model > polymer > >> system. Currently, I do following steps manually: > >> step 1) I run an energy minimization for a configuration. (using mdrun > >> option) > >> step 2) From the output of this configuration, I change something in the > >> coordinate file then run the energy minimization. (using editconf > option) > >> > >> I want to automate this process since the delay between runs is ~15 > >> minutes. My idea is that I can probably introduce time delay in scripts, > but > >> it would be nice if there's an option in GROMACS which allows for a > sequence > >> of mdruns. Does anyone aware of such option for GROMACS? > > > > No, this just sounds like a job for a simple for-loop. No time delay > > necessary, just set a counter for the number of iterations and run the > > sequence of commands within the loop. > > > > -Justin > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- > > gmx-users mailing list gmx-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 > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing list gmx-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 >
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