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We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields.…

DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…

The fast multipole method (FMM) has received growing attention in the beam physics simulation. In this study, we formulate an interpolation-based FMM for the computation of the relativistic space-charge field. Different to the…

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…

Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…

Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…

Active proteins and membrane-bound motors exert force dipole flows along fluid interfaces and lipid bilayers. We develop a Hamiltonian framework for the interactions of pusher and puller dipoles embedded in an incompressible two-dimensional…

Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…

Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…

While there have been many developments in computational probes of both strongly-correlated molecular systems and machine-learning accelerated molecular dynamics, there remains a significant gap in capabilities in simulating accurate…

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…

Simulating hybrid magnonic quantum systems remains a challenge due to the large disparity between the timescales of the two systems. We present a massively parallel GPU-based simulation framework that enables fully coupled, large-scale…

GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries…

Simulating the long-time evolution of Hamiltonian systems is limited by the small timesteps required for stable numerical integration. To overcome this constraint, we introduce a framework to learn Hamiltonian Flow Maps by predicting the…

Learning to simulate complex physical systems from data has emerged as a promising way to overcome the limitations of traditional numerical solvers, which often require prohibitive computational costs for high-fidelity solutions. Recent…

We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…

We present a GPU-accelerated cosmological simulation code, PhotoNs-GPU, based on algorithm of Particle Mesh Fast Multipole Method (PM-FMM), and focus on the GPU utilization and optimization. A proper interpolated method for truncated…

Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…

Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…

Improving time-to-solution in molecular dynamics simulations often requires strong scaling due to fixed-sized problems. GROMACS is highly latency-sensitive, with peak iteration rates in the sub-millisecond, making scalability on…