Accelerating the 3D reference interaction site model theory of molecular solvation with treecode summation and cut-offs.

The 3D reference interaction site model (3D-RISM) of molecular solvation is a powerful tool for computing the equilibrium thermodynamics and density distributions of solvents, such as water and co-ions, around solute molecules. However, 3D-RISM solutions can be expensive to calculate, especially for proteins and other large molecules where calculating the potential energy between solute and solvent requires more than half the computation time. To address this problem, we have developed and implemented treecode summation for long-range interactions and analytically corrected cut-offs for short-range interactions to accelerate the potential energy and long-range asymptotics calculations in non-periodic 3D-RISM in the AmberTools molecular modeling suite. For the largest single protein considered in this work, tubulin, the total computation time was reduced by a factor of 4. In addition, parallel calculations with these new methods scale almost linearly and the iterative solver remains the largest impediment to parallel scaling. To demonstrate the utility of our approach for large systems, we used 3D-RISM to calculate the solvation thermodynamics and density distribution of 7-ring microtubule, consisting of 910 tubulin dimers, over 1.2 million atoms.

The numerical evaluation of Slater integrals on graphics processing units.

This article presents SlaterGPU, a graphics processing unit (GPU) accelerated library that uses OpenACC to numerically compute Slater-type orbital (STO) integrals. The electron repulsion integrals (ERI) are computed under the RI approximation using the Coulomb potential of the Slater basis function. To fully realize the performance capabilities of modern GPUs, the Slater integrals are evaluated in mixed-precision, resulting in speedups for the ERIs of over 80×. Parallelization on multiple GPUs allows for integral throughput of over 3 million integrals per second. This places STO integral throughput within reach of single-threaded, conventional Gaussian integration schemes. To test the quality of the integrals, the fluorine exchange reaction barrier in fluoromethane was computed using heat-bath configuration interaction (HBCI). In addition, the singlet-triplet gap of cyclobutadiene was examined using HBCI in a triple- ζ , polarized basis set. These benchmarks demonstrate the library's ability to generate the full set of integrals necessary for configuration interaction with up to 6 h functions in the auxiliary basis.

Comparison of the MSMS and NanoShaper molecular surface triangulation codes in the TABI Poisson-Boltzmann solver.

The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of solvated biomolecules. In this model the dielectric interface between the biomolecule and solvent is often taken to be the molecular surface or solvent-excluded surface (SES), and the quality of the SES triangulation is critical in boundary element simulations of the model. This work compares the performance of the MSMS and NanoShaper surface triangulation codes for a set of 38 biomolecules. While MSMS produces triangles of exceedingly small area and large aspect ratio, the two codes yield comparable values for the SES surface area and electrostatic solvation energy, where the latter calculations were performed using the treecode-accelerated boundary integral (TABI) PB solver. However we found that NanoShaper is computationally more efficient and reliable than MSMS, especially when parameters are set to produce highly resolved triangulations.

TABI-PB 2.0: An Improved Version of the Treecode-Accelerated Boundary Integral Poisson-Boltzmann Solver.

This work describes TABI-PB 2.0, an improved version of the treecode-accelerated boundary integral Poisson-Boltzmann solver. The code computes the electrostatic potential on the molecular surface of a solvated biomolecule, and further processing yields the electrostatic solvation energy. The new implementation utilizes the NanoShaper surface triangulation code, node-patch boundary integral discretization, a block preconditioner, and a fast multipole method based on barycentric Lagrange interpolation and dual tree traversal. Performance-critical portions of the code were implemented on a GPU. Numerical results for protein 1A63 and two viral capsids (Zika, H1N1) demonstrate the code's accuracy and efficiency.

Improvements to the APBS biomolecular solvation software suite.

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.