paper for details).
As shown below, we have substantially accelerated the code for the computation of the hydration site energy. This was achieved by implementing the calculation of the free volume fractions (the walpha quantities above) by using a pairwise summation over scaled atomic volumes rather than a full overlap volume calculation as done for the "self volumes" ). As for the other reported optimizations we further accelerated the code by vectorization techniques.
The calculation of the hydration site energy is ~10 times faster Relative to the previous implementation, The overall speed of the AGBNP2 code is now more than twice that of the original implementation (for the same number of interactions).