[gmx-users] sequence of mdrun commands

[Justin A. Lemkul]

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

-- 
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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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