grompp no longer modifies nstcomm

grompp will no longer set nstcomm, the interval for center of mass motion removal, equal to nstcalcenergy when nstcomm < nstcalcenergy. A note is still printed in that case.

Bonded atom types names can now start with a digit

Bonded atom types names in topologies were not allowed to start with a number. Now all names are supported that contain at least one non-digit character.

Issue 4120

Core spin-up code is removed

Formerly, on non-x86 and non-PowerPC platforms, mdrun ran some multi-threaded code to try to wake up any cores that the OS might have powered down. This caused problems on some Arm platforms, and does not seem to suit a significant number of platforms for use of GROMACS. So now it is removed.

If required, please manually spin-up the cores with, e.g., stress --cpu $(nproc --all).

Issue 4074

Add documentation for linear angle potential

Added documentation and reference for the linear angle potential. Also added please_cite entry, but there is no call to reference it yet.

Issue 4286

gmxapi.mdrun guarantees trajectory output

gmxapi simulations now always run with full-precision trajectory output (-o) in order to guarantee the availability of a usable output trajectory through the mdrun.output.trajectory result.

Issue 4285

gmxapi.mdrun accepts arbitrary runtime arguments

Arbitrary mdrun arguments can be passed through gmxapi with the new runtime_args key word argument, accepting a dictionary of flags and values.

Issue 4284