Avoiding the van der Waals Endpoint Problem Using Serial Atomic Insertion

In the past analyses of the so-called van der Waals end point problem focused on thermodynamic integration. Here we investigate which of the recommendations, such as the need for soft-core potentials, are still valid when Bennett's acceptance ratio method is used. We show that in combination with Bennett's acceptance ratio method intermediate states characterized by the coupling parameter lambda can be replaced by intermediate states in which Lennard-Jones interactions are turned on or off on an "atom by atom" basis. By doing so, there is no necessity to use soft-core potentials. In fact, one can compute free energy differences without dedicated code, making it possible to use any molecular dynamics program to compute alchemical free energy differences. Such an approach, which we illustrate by several examples, makes it possible to exploit the tremendous computational power of the graphics processing unit. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2449-2458, 2011