Default SD integrator is now sd1 by Nicu Goga

The default SD integrator is now sd1, sd2 is deprecated. grompp
and mdrun both warn about sd2, and recommend sd.

The new sd1 integrator was developed by Herman Berendsen and
implemented by Nicu Goga.
Without constraints the sd1 integrator is nearly unchanged.
With constraints the new sd1 integrator is now as accurate as normal
MD with a leap-frog integrator, whereas the sd2 integrator will give
a slightly too high temperature.

Fixes #1496

Change-Id: I02b4537b05742ed499a84b625c4d4bf8994c0304