Point biobb to a manually compiled version of Gromacs

[JSLJ23]

Is there a way to:

1. Install this biobb but with just the python components?
2. Point this biobb to a more recent manually compiled version of Gromacs?

[gbayarri]

Hi @JSLJ23 !

Thanks for using BioExcel Building Blocks.

Yes, you can install only the python components for a biobb package. For installing just the python components, you can install the biobb packages via pip:

https://pypi.org/project/biobb-gromacs/

Be aware that, if you don't install biobb_gromacs via conda, you must install biobb_common (a conda dependency for this package) manually as well:

https://pypi.org/project/biobb-common/

And then be sure that both of them are in the same python virtual environment. Otherwise, maybe you should modify the paths to biobb_common in all the biobb_gromacs tools that you are using.

As for the manually compiled version of GMX, in all the biobb tools you have a common property named _binarypath that, in the case of the biobb_gromacs tools, must be the path to your local GMX path. Ie:

https://biobb-gromacs.readthedocs.io/en/latest/gromacs.html#module-gromacs.grompp

If you have problems with the pip installation, I would recommend you to do the installation via conda and use the _binarypath for executing your GMX instead of the one inside the conda environment.

Hope this helps.