I have been using IPython for scientific computing recently and was curious if it could be beneficial for the researchers that run MD simulations. Unfortunately I am not a specialist at this topic: I have 0 publications in this particular field. Nevertheless, I attempted to show how one can use IPython with Gromacs:
https://github.com/lupoglaz/GromacsIPython
And I would like to ask you to judge if the integration of these two tools is a worthy project.
It's never a bad idea to build tutorials, especially using IPython notebooks. Once you're done, put them on the ipython wiki:
https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks
I started using using iPython just to use the MDtraj library to analyze trajectories. THere's definitely a learning curve and required mindset, but I'm finding that the integration of clustering and inline plots are really helpful. I'm sure that one can really tie stuff together better, but baby steps….
Thank you for your answers! I will continue my attempts to fuse these two utilities, in particular:
1. Add gromacswrapper
2. Make my notebooks for MARTINI models public (one can have some difficulties in making visualizations of MARTINI models with python, therefore I wrote simple scripts that use VMD to do this)
3. Add short error notifications
Anyway, your interest and examples of use of ipython notebook in real-case studies showed me that it is worth spending time on related projects.
Thank you!
Looks nice. I use our own MDAnalysis and GromacsWrapper a lot from ipython (but looking at your code, you've already discovered GromacsWrapper yourself). The latter is basically syntactic sugar so that you can pretend that the Gromacs tools are Python functions, e.g. you can write gromacs.editconf(f="input.gro", o="output.pdb"). It might make your nice notebooks even more readable. GromacsWrapper also has a class to work with XVG files (gromacs.formats.XVG) that might be useful.
http://mdanalysis.googlecode.com/
http://orbeckst.github.io/GromacsWrapper/
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