[gmx-users] sequence of mdrun commands

Yongchul Chung yxc169 at case.edu
Thu Aug 25 20:59:31 CEST 2011

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
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?

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