Related papers: Molecular Dynamics with Conformationally Dependent…
Deposition of smaller granular particles on a larger nucleus particle has been simulated in two-dimension using molecular dynamics method. Variation of sequences of velocity of deposited particles is conducted and reported in this work. The…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Computer simulation plays a central role in modern day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of…
The charge transfer and polarization effects are important components in the molecular mechanism description of bio-molecules. Classical force field with fixed point charge cannot take into the account of the non-negligible correlation…
The issues of electronic polarizability in molecular dynamics simulations are discussed. We argue that the charges of ionized groups in proteins, and charges of ions in conventional non-polarizable force fields such as CHARMM, AMBER,…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
The discovery and study of new material systems rely on molecular simulations that often come with significant computational expense. We propose MDDM, a Molecular Dynamics Diffusion Model, which is capable of predicting a valid output…
Atomic Force Microscopy (AFM) combined with electrical modes provides a powerful contactless approach to characterize material electrical properties at the nanoscale. However, conventional electrostatic models often overlook dynamic charge…
A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of…
Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Conventional molecular dynamics (MD) simulation approaches, such as $\textit{ab initio}$ MD (AIMD) and empirical force field MD (EFFMD), face significant trade-offs between physical accuracy and computational efficiency. This work presents…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Metastable condensed matter typically fluctuates about local energy minima at the femtosecond time scale before transitioning between local minima after nanoseconds or microseconds. This vast scale separation limits the applicability of…
The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (DCM), and solvated K$^+$ and Cl$^-$ ions. For the electrostatics, point charges (PCs) and machine…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
Constant-potential molecular dynamics (MD) simulations are indispensable for understanding the capacitance, structure, and dynamics of electrical double layers (EDLs) at the atomistic level. However, the classical constant-potential method,…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…