Support Membrane Protein in a3fe via Gromacs-based System Preparation

[Roy-Haolin-Du]

In A3FE, Gromacs is used for minimization, NVT, NPT, and ensemble equilibration.

For membrane protein systems, special .mdp parameters are required.
(e.g. Semi-isotropic pressure coupling required (XY ≠ Z directions); Different compressibility for membrane; Gentle pressure control to avoid membrane destabilization and so on....(sorry not familiar with these)

Currently, these parameters are not automatically included. But allow to custom gmx .mdp file for membrane systems in configuration generation step.

The code works as follows:

In a3fe, the run_heat_and_preequil_input and run_ensemble_equilibration functions all use run_process in system_prep.py, which internally runs GROMACS.

a3fe/a3fe/run/system_prep.py

Lines 8 to 9 in f8e1948

	"heat_and_preequil_input",
	"run_ensemble_equilibration",

In BioSimSpace, _gromacs.py, there's an extra_options field that allows you to pass additional parameters, which is handled inside the internal method _generate_config by using generateGromacsConfig function. https://github.com/OpenBioSim/biosimspace/blob/8ba863f612baee764c8b5935df9c40dbc2daef1e/python/BioSimSpace/Sandpit/Exscientia/Process/_gromacs.py#L425.
The detailed gromacs.mdp file is generated via generateGromacsConfig function in _config.py, where the extra_options are incorporated for membrane protein-specific control parameters. https://github.com/OpenBioSim/biosimspace/blob/8ba863f612baee764c8b5935df9c40dbc2daef1e/python/BioSimSpace/Sandpit/Exscientia/Protocol/_config.py#L421.

We aim to use gromacs to do minimization, nvt, npt and ensemble equilibration.

[Roy-Haolin-Du]

Temporary a3fe modification.
System Preparation (a3fe/run/system_prep.py):

class SystemPreparationConfig(_BaseModel):
    membrane_protein: bool = Fieldxxx  ### add mem pro config para
    def get_membrane_equilibration_config(self) -> dict: ### membrane pro config para
    def heat_and_preequil_input():
    def run_ensemble_equilibration():
    system = run_process(equilx, protocol, extra_options=cfg.get_membrane_equilibration_config()) ###NPT and equilibration with membrane support
    def run_process(extra_options: _Optional[dict] = None) ### add a new to let extra_options passed.
    process = _BSS.Process.Gromacs(system, protocol, work_dir=work_dir, extra_options=extra_options) #### BioSimSpace automatically merges extra_options into mdp via generateGromacsConfig

Then run:

import a3fe as a3
cfg = a3.SystemPreparationConfig(membrane_protein = True)
calc = a3.Calculation()
calc.setup(bound_leg_sysprep_config = cfg, free_leg_sysprep_config = cfg)
calc.run and analyse as usual...

Also, for the a3fe somd run part. SOMD support barostat_membrane.
https://github.com/OpenBioSim/sire/blob/67673e439ae17cbaca494c82b9d2db2d5fbcbdb3/wrapper/Tools/OpenMMMD.py#L271
Just change the template_config.cfg file

### Barostat ###
barostat = False
barostat_membrane = True

Future Enhancements：

1. Automatic membrane detection and temperature coupling groups (protein/membrane/solvent separation), also stable equilibration pressure protocols (Berendsen → Parrinello-Rahman).
2. BioSimSpace enhancements for native membrane config support for gromacs.