[gmx-users] sequence of mdrun commands

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 25 21:14:22 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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