Version 3.3.1

• pdb2gmx does not generate special bonds correctly. This affects for instance bonds between Heme groups and sidechains and possibly between Cystein residues. More info and a patch are available on bugzilla.
• the long-range contribution to the forces (due to PME/Ewald summation) is not taken into account when doing energy minimizations or normal mode analysis (fixed in CVS Aug 2006). This bug has most likely been present in most recent versions, including 3.2.x.

Version 3.3

• A bug in pme.c prevented simulations with pme_order != 4. A fix is available from the ftp site and of course in version 3.3.1.