[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs
João M. Damas
jmdamas at itqb.unl.pt
Fri May 6 18:21:53 CEST 2016
There is already a similar project going on for a long time:
On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda <pslacerda+gmx at gmail.com>
> Installation is now working. The upload script was broken.
> 2016-05-03 21:50 GMT-03:00 Pedro Lacerda <pslacerda+gmx at gmail.com>:
> > Hi Gromacs users,
> > I just started to develop a scripting framework for Gromacs, it makes
> > 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
> > 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.
> > https://github.com/pslacerda/gmx
> > 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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João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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