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
