writing simulation box to checkpoint file is broken in git head
Commit d5cb909 may have broken do_cpte_reals_low in src/gmxlib/checkpoint.c of git release-4-5-master head (8e1142c).
I observed that the end-of-trajectory .cpt file was far too small to have coordinates in it, and moreover mdrun segfaults as it is writing the box.
Since write_checkpoint and do_cpte_matrix make sure that list==NULL, do_cpte_reals_low writes nf when it is undefined. I can't tell what the fix should be.