Detailed description |
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The velocity Verlet integrator is by far the easiest to work with in allowing correct implementation of algorithms like simulated tempering, replica-exchange, or any other enhanced sampling algorithm that requires manipulation or redrawing of velocities. With leapfrog Verlet, we need to do a half-kick back in time to synchronize positions and velocities, make our modification, do a half-kick forward, and then re-SHAKE in order to obtain a correct starting point for further integration. This is very difficult to do correctly, so using velocity Verlet would fit better with OpenMM's "easy to use correctly" philosophy. |
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