This is just a note to say that this planned feature has been added to the OpenMM roadmap as a "farther-term" feature:

http://wiki.simtk.org/openmm/RoadmapTimeline

Per our discussion with Michael Shirts, it's likely that a "leapfrogized velocity Verlet" (from MRS):

1. evaluate force (positions are at t)
2. half kick velocity (from t-dt/2 to t)
3. constrain velocities to position at t.
-Insert temperature and pressure control here-
4. full kick position (from t to t+dt)
5. half kick velocities (from t to t+dt/2)
6. Constrain positions at t+dt, use the lagrange multipliers to constrain the velocities at t+dt/2

Where:

Step 2: v(t) = v(t-dt/2) + dt/2 a(t)
Step 4: x(t+dt) = x(t) + dt/2 v(t) + dt^2/2 a(t)
Step 5: v(t+dt/2) = v(t) + dt/2 a(t)

Now, one can actually reverse steps 4 and 5, and do:

Step 4: v(t+dt/2) = v(t) + dt/2 a(t)
Step 5: x(t+dt) = x(t) + dt/2 v(t+dt/2)

This looks a lot more like leapfrog; the only difference is the insertion of a constraint step between the velocity increments; in the case of pressure or temperature control, then the control steps are performed at this place as well.