added minimization and equilibration based on openmmtools run_gentle_equilibration

[NDoering99]

Changes made:

• Added the run_gentle_equilibration function to OpenMMDL, based on the implementation in openmmtools.
• This function performs energy minimization followed by a gentle, staged equilibration protocol prior to production MD simulations.
• The implementation was adapted to integrate with the existing OpenMMDL setup.
• This provides a standardized system preparation step, helping remove steric clashes and gradually relax the system before running production trajectories.