Update example old mdp file in user guide.

Update example old mdp file in user guide.

Update mdp file in user guide. Remove obsolete parameters, and choose parameters
that will not give error and warning by default. Also remove the contents of
mdout.mdp, since the user can easily retrieve that with the given command, and
the file is now much larger. Add note on parameters being dependent on force
fields. Fixes #1774.

Change-Id: I2d5f1cfcf933275f95352c25891ee0792944212c