Fix for trjconv preserving box dimensions.

Fix for trjconv preserving box dimensions.

When using -1 in the -box specification, box vectors were
instead set to zero rather than being preserved due to
clear_mat(fr.box). Now, fr.box is conditionally cleared to
prevent this.  A fatal error is triggered if the user is
trying to preserve a non-existent box to avoid repeating the
undesired behavior.

Change-Id: I7484c33a7db445e0ad7cf21b2694150eee9ef768