Open a-ws-m opened 2 months ago
The include = -I. -I..
line is always added so it's always present as an mdp_kwarg. However, any mdp_kwargs that have not been used are assumed to be options for gmx grompp
https://github.com/Becksteinlab/GromacsWrapper/blob/463820c492fd2bdf989040626bf99514df605ff9/gromacs/setup.py#L881-L882
It's very ugly hack but about 15 years ago I couldn't think of anything better and obviously haven't thought about it since then.
So if you get gmx grompp -include ...
(which you could verify by writing a log file with
gromacs.start_logging()
before your code starts) then I think the reason is that whatever you are using as a template for the MDP file does not contain a line
include = ...
Thus, the gw code above does not find a line in the mdp file to edit with the include
, the include key is not removed from the kwargs dict, and check_mdpargs()
finds stuff that it then repurposes as commandline options.
I'd try adding a include
line to your MDP file.
When I use
gromacs.setup.energy_minimize()
orgromacs.setup.MD()
, I get the following error:If I remove the contents of
gromacs.cbook.add_mdp_includes()
, the code works fine. Presumably it's necessary for some use cases, but I think the arguments need to be added to the MDP file, rather than on the command line.