Fix tests that were unstable or too long

Some freeenergy tests were taking too long.

simple_search_group was unstable, so converted it and simple_search to
be better behaved. The boxes they use are uncomfortably small, so the
cutoffs need to be small also.

relative was also unstable, occasionally failing on bs_nix1004 and
another Jenkins slave around step 17. That suggests the step 10
neighbour search was not reproducible enough.

Also shortened the freenergy/relative simulation
(keeping nstdhdl with at least two nstlist calls between).

Fixes #1370

Change-Id: I14c8414dd03ba340babe289bc0860fe89e803f3c