[gmx-developers] [biosimgrid-team] Python interface connecting Gromacs and BioSimGrid

[Erik Lindahl]

Hi Kaihsu,
>
> We are currently looking into building an automated
> interface to deposit trajectories from GROMACS (and from
> other simulation code) into BioSimGrid, whose backend is a
> commodity relational database.

Great - that sounds exciting!

> Several options are worth considering:
> 1) Using the command-line GROMACS tools to parse xtc files
>    and piping it into another programme (in any language).

Right - this solution is somewhat ugly, but it will work immediately.

> 2) Linking to the GROMACS C-based libraries.  This limits us
>    to C.

Actually, you're not limited to C, only languages that can call C-style 
functions, but that includes: C, C++, Fortran, Java, Perl, Python, etc 
- almost anything.

This is the main reason we stick to C in the code instead of moving to 
C++ - portability, and the option of using non-object-oriented 
languages.

> 3) Involving Python.
> Since we already use Python on the analyses front of our
> project, we are interested in exploring option 3.  Rumour
> has it that there is a Python interface to GROMACS being
> developed.  Would you please tell us more about it?
>

Sure, although it still isn't finished. The main idea is to use the 
ability of C to interface with Python (see e.g. pymol for an excellent 
example). Each program (and several other routines) will be converted 
into a reasonably clean C function with arguments for all files and 
options. We will then write small python wrapper scripts for all the 
current analysis tools, so they work in almost the same way.

David is the main force behind this, but if you want to help he might 
need a hand with converting functions. Drop him a line at 
spoel at xray.bmc.uu.se (I think he's at a conference this week).

Cheers,

Erik