[gmx-users] GMXSCRIPT: Simple checkpointed Python scripting framework for Gromacs
peter.stern at weizmann.ac.il
Sat May 7 05:16:47 CEST 2016
I guess that Pedro clearly knows that since he refers to it on his page and explains why his is different.
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:
> 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.
>>> 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
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
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