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

[Peter Stern]

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
>> 
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>> 
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
> 
> 
> 
> -- 
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
> Tel:+351-214469613
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.