Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization
It passes my pycharm tests, except for virtual sites that I still need to correct + the reading of the masses is incorrect in some cases.
Masses can be present in the ITP of the molecule AND/OR in the ITP of the force field. Probably the masses that GMX uses are the ones present in the last #include in the TOP file.
For virtual sites, the main issues is that we need to consider that they are mapped in the NDX file, which is NOT the case atm. Then we need to act accordingly.
It passes my pycharm tests, except for virtual sites that I still need to correct + the reading of the masses is incorrect in some cases.
Masses can be present in the ITP of the molecule AND/OR in the ITP of the force field. Probably the masses that GMX uses are the ones present in the last #include in the TOP file.
For virtual sites, the main issues is that we need to consider that they are mapped in the NDX file, which is NOT the case atm. Then we need to act accordingly.