Questions and Answers

Various questions and answers that came up.

Is GromacsWrapper still maintained?

Yes, but development is sporadic.

For questions/problems please use the issue tracker; you can add @orbeckst to get the attention of the primary developer/bug fixer; please use the issue tracker instead of private email.

Feel free to contribute, pull requests are very welcome!

What can I do if my Gromacs commands are named differently?

From issue #124:

Question (@theavey)

My installation of gromacs has commands named, for example, gmx_mpi (all ending _mpi). These then get used in this tools as, for example, gromacs.grompp_mpi. This normally works fine for me, but when trying to import romacs.setup, there are two commands that are issues: one on line 585 of cbook.py and one on line 163 of setup.py. One calls tools.Grompp (which for me needed to be tools.Grompp_mpi) and the other calls gromacs.tools.Trjconv (which needed to be gromacs.tools.Trjconv_mpi).

I'm not sure if there is a way to automatically find what these should be called based on how the functions are defined, or if this is just something I need to deal with (and manually fix) because of my differently-named gromacs commands.

Answer (@orbeckst)

I can't think of a pretty way to fix this. If you know of a good way to handle this let me know!

However, I can think of a really rough way: Before you start, make aliases for the offending commands:

import gromacs
gromacs.tools.Grompp = gromacs.tools.Grompp_mpi
gromacs.tools.Trjconv = gromacs.tools.Trjconv_mpi