Miscellaneous

Renamed all NBNXN environment variables to NBNXM

All environment variables starting with GMX_NBNXN have been renamed to start with GMX_NBNXM for consistency with the algorithm’s name.

Replaced usage of custom Bohr radius value in gmx spatial with the common value from units

The gmx spatial command used to have its own definition of Bohr radius. For consistency with other parts of GROMACS, it now uses the definition of Bohr radius from the same source as the rest of the code. Notably, the value of the constant changed from 0.529177249 (IUPAC 1999) to 0.529177210903 (NIST 2018).

AMBER19SB and AMBER14SB force fields now use IUPAC standard hydrogen names

gmx pdb2gmx now recognizes the hydrogen names from the force field rather than always starting from 1. This means that the AMBER19SB and AMBER14SB force fields now use the original hydrogen names, (i.e. HB2 and HB3 for methylene hydrogens instead of HB1 and HB2). This is more consistent with the naming in the original Amber force field files and with the IUPAC standard for hydrogen names.