[gmx-users] sequence of mdrun commands

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Aug 25 22:14:16 CEST 2011

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 [...] &
grompp [...]
mdrun -deffnm [...] &

Hope it helps,


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
> 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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