Related papers: RUMD: A general purpose molecular dynamics package…
PLUMED-GUI is an interactive environment to develop and test complex PLUMED scripts within the Visual Molecular Dynamics (VMD) environment. Computational biophysicists can take advantage of both PLUMED's rich syntax to define collective…
In this paper we describe and demonstrate a C++ code written to determine the trajectory of particles traversing oriented single crystals and a CUDA code written to evaluate the radiation spectra from charged particles with arbitrary…
The future of computation is the Graphical Processing Unit, i.e. the GPU. The promise that the graphics cards have shown in the field of image processing and accelerated rendering of 3D scenes, and the computational capability that these…
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…
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an…
We present LBcuda, a GPU accelerated version of LBsoft, our open-source MPI-based software for the simulation of multi-component colloidal flows. We describe the design principles, the optimization and the resulting performance as compared…
High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Graphics Processing Units (GPUs) leverage massive parallelism and large memory bandwidth to support high-performance computing applications, such as multimedia rendering, crypto-mining, deep learning, and natural language processing. These…
A micromagnetic simulator running on graphics processing unit (GPU) is presented. It achieves significant performance boost as compared to previous central processing unit (CPU) simulators, up to two orders of magnitude for large input…
Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…
Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing…
High-performance graphical processing units (GPU) are used for the repeated parallelised propagation of non-linear partial differential equations on large spatio-temporal grids. The main challenge results as a combination of the requirement…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
As heterogeneous supercomputing architectures leveraging GPUs become increasingly central to high-performance computing (HPC), it is crucial for computational fluid dynamics (CFD) simulations, a de-facto HPC workload, to efficiently utilize…
We present our implementation of the RHMC algorithm for staggered fermions on Graphics Processing Units using the NVIDIA CUDA programming language. While previous studies exclusively deal with the Dirac matrix inversion problem, our code…
Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…
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…
The SIMT execution model is commonly used for general GPU development. CUDA and OpenCL developers write scalar code that is implicitly parallelized by compiler and hardware. On Intel GPUs, however, this abstraction has profound performance…
The two main thrusts of computational science are more accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g.…