Gmx-mmpbsa

Fixed minor issues in gmx_MMPBSA and gmx_MMPBSA_ana
Implemented the custom mask atom selection for qm-charge
Fixed inconsistencies with the installation process and the dependencies

Fixed minor issues

Fixes

- PB decomp ends in error (https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/352)
- Better parsing for errors

Additions
- GBNSR6 model implementation
- Enthalpy
- Per-residue and Per-wise decomposition
- Documentation and examples
- Added git dependency to env.yml file
- Groups can now be defined as either the number or the name (157)
- Added error tracking for groups that are not in the index file

Fixes
- Incompatible `compilers` version
- Fixed bug when CAS and PB/RISM calculations are performed
- Fixed duplicated options and args checking
- Documentation improved
- Fixed numpy deprecated np.float (316)
- Fixed reproducible command line in debugging in log file (335)
- GROMACS 2023 compatibility (327, 335)
- Fixed IE and C2 Entropy (325)
- PyMOL doesn't open within gmx_MMPBSA environment (331)
- Inaccessible _temp_top.top when the topology file is in different directory (299)

Changes
- A copy old info file is created when rewrite-output (for backward compatibility)
- Setting inp = 1 by default (329)

**Additions**
- Progress bar implementation
- verbose options for API and info logging for IE and C2 entropy calculations
- Added logging info for MPI calculations

**Fixes**
- QH entropy calculation
- Decomposition bug (269)
- Alanine scanning in Terminal residues
- Regression to output files subwindow in gmx_MMPBSA_ana
- Bug when using the compact results version
- Seaborn compatibility
- `print_res` in `&decomp` namelist does not accept "all" (292)
- error when output files are open and any plot property is changed
- error if at least one residue of both the receptor and the ligand is not included in the selection for decomposition

**Changes**
- now use `mpi4py` when `mpi_size > 1` otherwise use `fake_MPI`. Now "MPI" flag is not required

Fix

gmx_MMPBSA

- Inconsistent decomposition output (246, 248)
- IE and C2 entropies calculation fail when rewrite-output (253)
- Delta Delta Entropies' values are incorrect (257)
- Loading binary file fails when alanine scanning is performed (258)

gmx_MMPBSA_ana

- Mutant-Normal data is not computed or displayed (254)
- Inconsistent energy values in PyMol visualization (255)

Changes

gmx_MMPBSA

- Re-implementation of compact binary output file (249)