Treatment of pbc reference atoms

[BerndDoser]

When the diameter of the pull group is larger than half the shortest box vector, it could be necessary to define a reference atom for the pull group. Since the numbering of the groups is converted, RAMD provides own mdp parameters (ramd-group1-ligand-pbcatom and ramd-group1-receptor-pbcatom), which forwards the reference atom to the corresponding pull group. In addition the mdp parameter ramd-pbc-ref-prev-step-com is available, which forward to pull-pbc-ref-prev-step-com, however, with a different default value (yes).