Two questions on Important note of fix/bond create

its the same principle as for the other lists, there needs to be enough space reserved to handle new bonds, angles, dihedrals, special neighs, etc on a particular atom. if ‘extra special per atom’ is not used, then during the run particular atoms might or might not have enough space on the special list depending on your starting topology, how many bonds are formed, special settings, etc. for special list (and really all of these lists) i think the easiest thing to do is not to be cheap with memory and just assume that the extra space will be needed. there isn’t a requirement to use ‘extra special per atom’ but do be aware that the special list can overflow in the middle your run.