Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics

Charge transfer at the Bovine pancreatic trypsin inhibitor (BPTI) protein–water interface was analyzed by means of ab initio Born–Oppenheimer molecular dynamics simulation of the entire protein running on graphical processing units (GPUs). The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to perform these calculations on a desktop computer. Mulliken and Voronoi deformation density (VDD) population analysis reveals that between 2.0 and 3.5 electrons are transferred from surrounding water molecules to the protein over the course of the 8.8 ps simulation. Solving for the electronic structure of BPTI in the absence of surrounding water molecules (i.e., in the gas phase) leads to large intraprotein charge transfer, where approximately one electron in total is transferred from neutral to polar residues. Solvation relieves this polarization stress, leading to a neutralization of the excess positive charge of the neutral residues

Ab Initio Quantum Chemistry for Protein Structures

Structural properties of over 55 small proteins have been determined using both density-based and wave-function-based electronic structure methods in order to assess the ability of ab initio “force fields” to retain the properties described by experimental structures measured with crystallography or nuclear magnetic resonance. The efficiency of the GPU-based quantum chemistry algorithms implemented in our TeraChem program enables us to carry out systematic optimization of ab initio protein structures, which we compare against experimental and molecular mechanics force field references. We show that the quality of the ab initio optimized structures, as judged by conventional protein health metrics, increases with increasing basis set size. On the other hand, there is little evidence for a significant improvement of predicted structures using density functional theory as compared to Hartree–Fock methods. Although occasional pathologies of minimal basis sets are observed, these are easily alleviated with even the smallest double-ζ basis sets

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm–Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results)

Implementation of Scientific Computing Applications on the Cell Broadband Engine

The Cell Broadband Engine architecture is a revolutionary processor architecture well suited for many scientific codes. This paper reports on an effort to implement several traditional high-performance scientific computing applications on the Cell Broadband Engine processor, including molecular dynamics, quantum chromodynamics and quantum chemistry codes. The paper discusses data and code restructuring strategies necessary to adapt the applications to the intrinsic properties of the Cell processor and demonstrates performance improvements achieved on the Cell architecture. It concludes with the lessons learned and provides practical recommendations on optimization techniques that are believed to be most appropriate

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures