Bugs fixed

Fix double counting of dispersion correction with test particle insertion

The dispersion correction of the test particle with the system was double counted.

Issue 5231

gmx grompp now allows test particle insertion of an identical molecule

gmx grompp merges molecule blocks in the topology with the same molecule type. With TPI this prevented insertion of a molecule into a liquid of the same molecules.

Fix rare issue with missing perturbed exclusions error

In rare cases for system with perturbed pair interactions that are zero, e.g. a state with decoupled charges such that some hydrogens are non-interacting, gmx mdrun could exit with an error message stating that excluded, perturbed interactions are beyond the cut-off, whereas this was actually not the case.

Issue 5267