Related papers: Harvesting graphics power for MD simulations
We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a…
One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…
We present implementations of a fourth-order symplectic integrator on graphic processing units for three $N$-body models with long-range interactions of general interest: the Hamiltonian Mean Field, Ring and two-dimensional self-gravitating…
We investigate applicability of GPU to DEM. NVIDIA's code obtained superior performance than CPU in computational time. A model of contact forces in NVIDIA's code is too simple for practical use. We modify this model by replacing it with…
Purpose: Very fast Monte Carlo (MC) simulations of proton transport have been implemented recently on GPUs. However, these usually use simplified models for non-elastic (NE) proton-nucleus interactions. Our primary goal is to build a…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include 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,…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…
This paper presents a computationally efficient implementation of a Hamming code decoder on a graphics processing unit (GPU) to support real-time software-defined radio (SDR), which is a software alternative for realizing wireless…
The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…
Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the…
Parallel computing can offer an enormous advantage regarding the performance for very large applications in almost any field: scientific computing, computer vision, databases, data mining, and economics. GPUs are high performance many-core…
Graphics processing units (GPUs) are recently being used to an increasing degree for general computational purposes. This development is motivated by their theoretical peak performance, which significantly exceeds that of broadly available…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
Hardware accelerators (such as Nvidia's CUDA GPUs) have tremendous promise for computational science, because they can deliver large gains in performance at relatively low cost. In this work, we focus on the use of Nvidia's Tesla GPU for…
We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
Highly-parallel graphics processing units (GPUs) can improve the speed of micromagnetic simulations significantly as compared to conventional computing using central processing units (CPUs). We present a strategy for performing…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…