Related papers: A Simple Iterative Approach for Constant Chemical …
Neural network potentials (NNPs) offer a fast and accurate alternative to ab-initio methods for molecular dynamics (MD) simulations but are hindered by the high cost of training data from high-fidelity Quantum Mechanics (QM) methods. Our…
An improved numerical solver for the unified solution of compressible and incompressible fluids involving interfaces is proposed. The present method is based on the CIP-CUP (Cubic Interpolated Propagation / Combined, Unified Procedure)…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…
Machine learned interaction potentials (MLIPs) have become a critical component of large-scale, high-quality simulations for a range of chemical and biochemical systems. Yet, despite their in-distribution accuracy, molecular dynamics…
Scientific computing applications have benefited greatly from high performance computing infrastructure such as supercomputers. However, we are seeing a paradigm shift in the computational structure, design, and requirements of these…
Examination of thermal expansion of two-dimensional (2D) nanomaterials is a challenging theoretical task with either ab-initio or classical molecular dynamics simulations. In this regard, while ab-initio molecular dynamics (AIMD)…
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…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular…
For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force…
The growing interest in the dynamical properties of colloidal suspensions, both in equilibrium and under an external drive such as shear or pressure flow, requires the development of accurate methods to correctly include hydrodynamic…
Molecular-dynamics simulation can give atomistic information on the processes occurring in nanoindentation experiments. In particular, the nucleation of dislocation loops, their growth, interaction and motion can be studied. We investigate…
Incremental Potential Contact (IPC) is a widely used, robust, and accurate method for simulating complex frictional contact behaviors. However, achieving high efficiency remains a major challenge, particularly as material stiffness…
Implicit solvent, coarse-grained models with pairwise interactions can access the largest length and time scales in molecular dynamics simulations, owing to the absence of interactions with a huge number of solvent particles, the smaller…
As molecular scientists have made progress in their ability to engineer nano-scale molecular structure, we are facing new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs…
Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a combination of physics-based potentials with machine learning…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…