[gmx-users] sequence of mdrun commands

[Yongchul Chung]

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 <tsjerkw at 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 <jalemkul at 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
> >
> > ========================================
> > --
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>
>
>
> --
> 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
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