[BUG] [ABFE] ignore_warning=True NOT WORK for lam_vals

[ErikZhang-9762]

Describe the bug
In ABFE tutorials, ignore_warning option does not work for lam_vals,

Command line without -maxwarn parameter in gromacs.out.mdp file for lambda1-31,

Only work for lambda0.

All input files can be found in biosimspace_tutorials:

• github.com/OpenBioSim/biosimspace_tutorials/blob/main/04_fep/03_ABFE/01_setup_abfe.ipynb

Hopefully this can be fixed!

[lohedges]

Thanks for reporting. This is an easy fix. The issue is that when using setup_only=True a BioSimSpace.Process.Gromacs object is only created for the first lambda window, then inputs are copied to the other directories and the lambda value is updated. We use grompp to recreate the binary run file, but have forgotten to apply the addtional user flags that would be passed to the process.