Movement of pull group COM atom of a large pull group can cause crashes
If the pull group COM atom moves so much that parts of the pull would jump would jump to the next periodic image the pull group COM will jump as well. This is related to Change-Id: Ida7004624a470981d9ce22a1ef921daebad83364, but not completely fixed by that commit. Example
A system that is 10 nm in the Z direction with a pull group that consists of lipid tails in the central 6 nm of the system with its pull group COM in the center of the system (i.e. 3 nm to the respective boundaries of the pull group). This does not violate Change-Id: Ida7004624a470981d9ce22a1ef921daebad83364. If, during the simulation, the COM atom would move more than 2 nm in the Z direction there will be issues with the COM location.
Allow using COM of previous step as PBC reference
Add an option, when pulling, to use the COM of the group of
the previous step, to calculate PBC jumps, instead of a reference
atom, which can sometimes move a lot during the simulation. When
there is no previous step (when the COM of the previous step is
not set) use the COM based on the reference atom. The COM of the
previous step is written to the checkpoint.