Related papers: Breaking the Molecular Dynamics Timescale Barrier …
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
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…
Material properties are fundamentally dictated by multiscale phenomena, which often reach mesoscale in size. The {\mu}m mesoscale is also the size which can be observed directly under an optical microscope, bridging the atomistic…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF)…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
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…
Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…
Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
We present the GPU version of DeePMD-kit, which, upon training a deep neural network model using ab initio data, can drive extremely large-scale molecular dynamics (MD) simulation with ab initio accuracy. Our tests show that the GPU version…
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…
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…
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We report scaling results on the world's largest supercomputer of our recently developed Billions-Body Molecular Dynamics (BBMD) package, which was especially designed for massively parallel simulations of the atomic dynamics in structural…
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…
Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…