Thanks Justin, and Tsjerk for the helpful comments. I think I can get away with a simple for-loop as Justin recommended.<div><br></div><div>Greg</div><div><br><br><div class="gmail_quote">On Thu, Aug 25, 2011 at 4:14 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hey :<br>
<br>
In scripts, like on the command line, processes wait for earlier<br>
processes to finish, unless these are brought to the background using<br>
the ampersand '&' at the end of the line. If you want to execute<br>
something in the background in your script, to allow checking the<br>
progress automatically, for instance, you can make sure some later<br>
process does not start before the ones in the background finished by<br>
using the command 'wait':<br>
<br>
mdrun -deffnm [...] &<br>
wait<br>
grompp [...]<br>
mdrun -deffnm [...] &<br>
wait<br>
echo FINISHED<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Thu, Aug 25, 2011 at 9:14 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> Yongchul Chung wrote:<br>
>><br>
>> Hello gmx-users,<br>
>><br>
>> I am trying to run a sequence of energy minimizations for a model polymer<br>
>> system. Currently, I do following steps manually:<br>
>> step 1) I run an energy minimization for a configuration. (using mdrun<br>
>> option)<br>
>> step 2) From the output of this configuration, I change something in the<br>
>> coordinate file then run the energy minimization. (using editconf option)<br>
>><br>
>> I want to automate this process since the delay between runs is ~15<br>
>> minutes. My idea is that I can probably introduce time delay in scripts, but<br>
>> it would be nice if there's an option in GROMACS which allows for a sequence<br>
>> of mdruns. Does anyone aware of such option for GROMACS?<br>
><br>
> No, this just sounds like a job for a simple for-loop. No time delay<br>
> necessary, just set a counter for the number of iterations and run the<br>
> sequence of commands within the loop.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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><br>
<br>
<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
<div><div></div><div class="h5">--<br>
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