AGBNP2 Hydration Sites Energy Optimization

Post date: Apr 10, 2015 12:42:29 AM by Emilio Gallicchio

The AGBNP2 implicit solvent model represents short-range hydration effects, such as hydrogen-bonding to water, by means of so-called hydration sites. Each hydration site is represented as a sphere attached to the atoms on the surface of the solute. The model computes on the fly the fraction of the volume of hydration sites not occupied by solute atoms. This "free volume" fraction is then multiplied by adjustable hydration sites strength parameters that depend on the type of hydration site (hydrogen bond donor, acceptor, etc.--see the original 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.

Hydration Sites Overall



T4-Lysozyme + Chlorophenol

trp cage

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).

Support from the National Science Foundation is gratefully acknowledged