15 papers · ranked by Valyu relevance
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Christopher Myers, Ken Miyazaki, Thomas Trepl, Christine Isborn + 1 more
GPU-accelerated on-the-fly nonadiabatic dynamics is enabled by interfacing the linearized semiclassical dynamics approach with the TeraChem electronic structure program. We describe the computational workflow of the "PySCES" code interface, a Python code for semiclassical dynamics with on-the-fly electronic structure…
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Accurate and efficient prediction of electronic band structures is essential for designing materials with targeted properties. However, existing machine learning models often lack universality and struggle to predict detailed electronic structures, while traditional tight-binding models based on the Slater-Koster (SK)…
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Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
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The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
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An automatic code generated C++/HIP/CUDA implementation of the (auxiliary) Fock, or Kohn–Sham, matrix construction for execution in GPU-accelerated hardware environments is presented. The module is developed as part the quantum chemistry software package VeloxChem, employing localized Gaussian atomic orbitals. The per-…
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Modeling multimetallic systems efficiently enables faster prediction of desirable chemical properties and design of new materials. This work describes an initial implementation for performing multireference wave function method localized active space self-consistent field (LASSCF) calculations through the use of…
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Machine learning interatomic potentials (MLIPs) have revolutionized molecular simulations, but as they evolve, so does the demand for advanced computing architectures, particularly graphics processing units (GPUs). However, the high cost of GPUs limits accessibility, making it crucial to compare GPU and central…
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Electrostatic preorganization is an exciting mode to understand the catalytic function of enzymes, yet limited tools exist to computationally analyze it. In particular, no methods exist to interpret the geometry, dynamics, and fundamental components of 3-D electric fields, E(r), in protein active sites. Here we present…
Toni Sivula, Laxman Yetukuri, Tuomo Kalliokoski, Heikki Käsnänen + 2 more
The emergence of ultra-large screening libraries, filled to the brim with billions of readily available compounds, poses a growing challenge for docking-based virtual screening. Machine Learning (ML) boosted strategies like the tool HASTEN combine rapid ML prediction with the brute-force docking of small fractions of…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We detail a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We then introduce the new "dual-water" mode and its use with the flexible AMOEBA…
Fréderic Célerse, Theo Jaffrelot-Inizan, Louis Lagardère, Olivier Adjoua + 4 more
We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs -accelerated implementation within Tinker-HP. For the specific use with the flexible AMOEBA polarizable force field (PFF), we introduce the new "dual–water" GaMD…
Althea Hansel-Harris, Andreas Tillack, Diogo Santos-Martins, Matthew Holcomb + 1 more
Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries. As such, it has become an increasingly common approach in early-stage drug discovery. These screenings generate large amounts of data proportional to the size of the compound library used, which must…
Pavel Pokhilko, Evgeny Epifanovsky, Anna I. Krylov
Using single precision floating point representation reduces the size of data and computation time by a factor of two relative to double precision conventionally used in electronic structure programs. For large-scale calculations, such as those encountered in many-body theories, reduced memory footprint alleviates…
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We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss-Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and treecode method, we utilize the Gauss-Legendre quadrature for integration over a finite range and spherical t-design for…