[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs

Pedro Lacerda pslacerda+gmx at gmail.com
Wed May 4 02:51:16 CEST 2016

Hi Gromacs users,

I just started to develop a scripting framework for Gromacs, it makes some
assumptions about the directory structure and command parameters. You
cannot prepare or run two different systems in the same directory and
always pass the -deffnm option to mdrun.

It is very nice!

Its main goal is to easy the reproduction of simulation protocols,
canonical steps used to perform and analyze a simulation. The commands are
stored in very readable and structured Python file that requires no
programming knowledge except syntax. Of course you can always extend it
with code as you need.

As a bonus it maintain in the .gmx/ directory a checkpoint file that skip
previously successful commands if started again. Also there is no need to
source GMXRC in common cases.


Please make comments, suggestions and critics about GMXSCRIPT. The next
feature would be an option to generate a file that allows to reproduce a
simulation in any linux computer with Gromacs installed.

(apologies for my poor English!)

Best regards,
Pedro Lacerda

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