Quantum supercharger library: Hyper-parallel integral derivatives algorithms forab initioQM/MM dynamics

Abstract

This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.

Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes

“…The past few years have witnessed an intense renewal of interest for force-field refinement procedures. This is in large part due to a number of computational and methodological advances − that have enabled an increased accuracy, automation, and throughput of these procedures, including more powerful processors and coprocessors (graphics processing units (GPUs) − and field-programmable gate arrays (FPGAs) − ), faster algorithms and improved simulation methodologies ( e.g ., for nonbonded interactions − and free-energy calculations − ), more accessible experimental data − (online literature and databases), and faster QM calculation codes. − In turn, these progresses have increased the practical usefulness of force-field-based simulations, in particular in the context of material and drug design, where approaches relying on atomistic MD simulations can nowadays keep pace with the fast time scale of industrial and pharmaceutical product development. − ,− …”

“…The HYFF and QDFF schemes are popular nowadays, in particular because they (i) benefit from fast QM calculation methods; − (ii) promise an exhaustive coverage of the chemical space; (iii) take into account induction effects on the PCs ,, as well as, possibly, on the LJ coefficients; ,,− ,, and (iv) are easier to automate in terms of topology construction and parameter derivation. The last point is of particular importance if large collections of molecules are to be considered in the calibration and/or application of the force field.…”

Multidimensional Free Energy and Accelerated Quantum Library Methods Provide a Gateway to Glycoenzyme Conformational, Electronic, and Reaction Mechanisms

“…The vast and complex conformational space that make glycans important functional units in cellular biology presents a computational modeling challenge to sufficiently sample hemiacetal phase space. ,, While the cellular processing of glycans via glycoenzymes (glycosyltransferases and glycosidases) are known drug targets of a wide range of communicable and noncommunicable diseases, unpacking the mechanistic details and designing new drugs requires commensurate ab initio level QM/MM tools to accurately simulate glycoenzyme catalytic action . The epimeric choices leading to variation in cyclic pyranose monomers, the ability of the pyranose rings to pucker into 38 distinct conformations, and the 5 or more functional groups bonded to the ring carbons that can rotate into distinct orientations (cis, trans, gauche) makes carbohydrates ideal for data storage and information transfer.…”

“…This not only overcomes the challenges of (i) robust sampling of phase space and (ii) accessible ab initio dynamics but when linked to a legacy code can leverage the historical analytic and simulation methods built into those codes. For these reasons, we developed a QM/MM polar bond link atom (SLASH) method as a library, a Free Energy and Reaction Dynamics (FEARCF) method , implemented as a library that when linked into MD packages comprehensively samples the phase space of pyranose puckering and glycoenzyme catalyzed, and a Quantum supercharger library that accelerates ab initio Quantum and QM/MM dynamics. , Here, we describe the FEARCF and QSL and demonstrate their unique features on a Hartree–Fock QM/MM reaction dynamics simulation of O -linked β- N -acetylglucosamine transferase ( O -GlcNAc or OGT).…”

Double‐buffered, heterogeneous CPU + GPU integral digestion algorithm for single‐excitation calculations involving a large number of excited states

“…The specific bottleneck depends upon the method in question, but these two potential bottlenecks have each been targeted for GPU acceleration. ERI generation was originally tackled on GPUs by Yasuda and by Martínez and coworkers, then later by others . In early work, there was difficulty extending GPU‐based ERI algorithms to basis sets with high angular momentum, as the intermediates required for computing high angular momentum shells were too large to store in GPU cache and registers, while the recursive nature of the integrals generation algorithm became rather complex for the “same instruction, multiple data” (SIMD)‐style operations where GPUs excel.…”