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

[Pedro Lacerda]

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 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.
>
>     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
>