Related papers: Long-range interactions & parallel scalability in …
We compare different Poisson solvers within the context of an electrostatic Vlasov-Poisson system. These schemes are implemented as part of the IPPL (Independent Parallel Particle Layer) library (Frey et al., 2024), which provides…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
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,…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
With the great development of parallel computing techniques, the particle-particle (PP) model has been successfully applied in a number of plasma applications. Comparing to particle-mesh (PM) models, for example the widely used…
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…
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…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
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…
We present a new scalable algorithm for short-range molecular dynamics simulations on distributed memory MIMD multicomputer based on a message-passing multi-cell approach. We have implemented the algorithm on the Connection Machine 5 (CM-5)…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
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…
The three most common methods, Ewald, fast multipole (FMM) and the particle-particle particle-mesh (PPPM), used to compute the interactions in many body Coulombic systems are compared for single and multi-processor machines. The Ewald…
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 push the boundaries of electronic structure-based \textit{ab-initio} molecular dynamics (AIMD) beyond 100 million atoms. This scale is otherwise barely reachable with classical force-field methods or novel neural network and machine…
High-performance computing (HPC) is reshaping computational drug discovery by enabling large-scale, time-efficient molecular simulations. In this work, we explore HPC-driven pipelines for Alzheimer's disease drug discovery, focusing on…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…