Related papers: Molecular Dynamics Simulation of Macromolecules Us…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
Most relatively modern desktop or even laptop computers contain a graphics card useful for more than showing colors on a screen. In this paper, we make a case for why you should learn enough about GPU (graphics processing unit) computing to…
In this proceedings we present MadFlow, a new framework for the automation of Monte Carlo (MC) simulation on graphics processing units (GPU) for particle physics processes. In order to automate MC simulation for a generic number of…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a million particles were conducted with a massively parallel MD…
Maximizing the performance potential of the modern day GPU architecture requires judicious utilization of available parallel resources. Although dramatic reductions can often be obtained through straightforward mappings, further performance…
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…
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…
We present in this paper our work regarding simulating a type of P system known as a spiking neural P system (SNP system) using graphics processing units (GPUs). GPUs, because of their architectural optimization for parallel computations,…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We present a single-node, multi-GPU programmable graph processing library that allows programmers to easily extend single-GPU graph algorithms to achieve scalable performance on large graphs with billions of edges. Directly using the…
Restricted solid on solid surface growth models can be mapped onto binary lattice gases. We show that efficient simulation algorithms can be realized on GPUs either by CUDA or by OpenCL programming. We consider a deposition/evaporation…
We implement a quantum optimal control algorithm based on automatic differentiation and harness the acceleration afforded by graphics processing units (GPUs). Automatic differentiation allows us to specify advanced optimization criteria and…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
Molecular Dynamics (MD) simulation is widely used to analyze the properties of molecules and materials. Most practical applications, such as comparison with experimental measurements, designing drug molecules, or optimizing materials, rely…
Graphics Processing Unit (GPU) computing is becoming an alternate computing platform for numerical simulations. However, it is not clear which numerical scheme will provide the highest computational efficiency for different types of…
Researchers in biology are faced with the tough challenge of developing high-performance computer simulations of their increasingly complex agent-based models. BioDynaMo is an open-source agent-based simulation platform that aims to…
Graphics Processing Units (GPUs) are high performance co-processors originally intended to improve the use and quality of computer graphics applications. Once, researchers and practitioners noticed the potential of using GPU for general…
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…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…