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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…
GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…
For many years, systems running Nvidia-based GPU architectures have dominated the heterogeneous supercomputer landscape. However, recently GPU chipsets manufactured by Intel and AMD have cut into this market and can now be found in some of…
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,…
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…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
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…
GROMACS is a de-facto standard for classical Molecular Dynamics (MD). The rise of AI-driven interatomic potentials that pursue near-quantum accuracy at MD throughput now poses a significant challenge: embedding neural-network inference into…
Simulations of biomolecules have enormous potential to inform our understanding of biology but require extremely demanding calculations. For over twenty years, the Folding@home distributed computing project has pioneered a massively…
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…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
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…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…
We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit…
-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…