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

[Pedro Lacerda]

Yes, GromacsWrapper doesn't enforces some project structure, it's more like
a library despite its name.
GmxScript enforces some kind of project organization. As GromacsWrapper,
it's not a huge advantage over pure shell scripts, except because every
command is checkpointed and is very readable.

Cheers,
Pedro Lacerda

2016-05-07 0:06 GMT-03:00 Peter Stern <peter.stern at weizmann.ac.il>:

> I guess that Pedro clearly knows that since he refers to it on his page
> and explains why his is different.
>
> Cheers,
> Peter
>
> Sent from my iPad
>
> > On May 6, 2016, at 12:22 PM, João M. Damas <jmdamas at itqb.unl.pt> wrote:
> >
> > There is already a similar project going on for a long time:
> > https://orbeckst.github.io/GromacsWrapper/
> >
> > Cheers,
> > João
> >
> > On Wed, May 4, 2016 at 3:12 AM, Pedro Lacerda <pslacerda+gmx at gmail.com>
> > wrote:
> >
> >> 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
> >> --
> >> Gromacs Users mailing list
> >>
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> >
> >
> >
> > --
> > João M. Damas
> > PhD Student
> > Protein Modelling Group
> > ITQB-UNL, Oeiras, Portugal
> > Tel:+351-214469613
> > --
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