GROMACS

g_sas computes incorrect surface areas if -nopbc is specified. The problem has been introduced some time in the 4.0.x series, probably between 4.0 and 4.0.3 (e2045413, merged to development version in 1437fac0). The cell size of the grid used to search for neighboring atoms is determined as the radius of the first atom instead of double the maximum radius as it should.

Additionally, the 4.0.x series g_sas always triggers the -nopbc option (ed04b50), irrespective of what is provided on the command line (and thus always produces the incorrect result).

This explains at least some of the results reported on gmx-users: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-February/087460.html