Frontiers in Computational Chemistry

Volume: 5

Implementation of the Molecular Electrostatic Potential over GPUs: Large Systems as Main Target

Author(s): J. César Cruz, Ponciano García-Gutierrez, Rafael A. Zubillaga, Rubicelia Vargas and Jorge Garza * .

Pp: 149-173 (25)

Doi: 10.2174/9789811457791120050006

* (Excluding Mailing and Handling)

Abstract

The molecular electrostatic potential (MEP) is a useful tool to design and develop drugs. However, the evaluation of this property using quantum chemistry methods presents a challenge for molecules of medium or large size since this is computationally expensive. In this chapter, we showed two implementations of this property over graphics processing units (GPU). In the first instance, we discussed some details that must be considered when GPUs are involved in high-performance computing. After this step, the algorithms considered to evaluate MEP over GPUs are exposed to observe the main differences between a method with minimal approximations and another one where usual approximations are implemented in many quantum chemistry codes. The benefits provided by these graphics cards are evidenced when our implementations are applied over molecules of considerable size like those found in protein-ligand complexes, where usually the electrostatic potential is modeled by a set of point charges.


Keywords: Cuda-C, GPUs, Molecular Electrostatic Potential, Multipolar Expansion, Proteins.

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