相关论文: Small ionic radii limit time step in Martini 3 mol…

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 determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…

Current molecular dynamic simulations of biomolecules using multiple time steps to update the slowingly changing force are hampered by an instability occuring at time step equal to half the period of the fastest vibrating mode. This has…

The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…

Ionic liquids constrained at interfaces or restricted in subnanometric pores are increasingly employed in modern technologies, including energy applications. Understanding the details of their behavior in these conditions is therefore…

We report on a molecular dynamics investigation of the wetting properties of graphitic surfaces by various solutions at concentrations 1-8 wt% of commercially available non-ionic surfactants with long hydrophilic chains, linear or T-shaped.…

We report here on the pitfalls of the simulation model introduced in the "Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field" [Journal of Chemical Theory and Computation 2018, 14, 11,…

Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force…

Molecular dynamics (MD) simulations are employed to investigate the capillary fluctuations of steps on the surface of a model metal system. The fluctuation spectrum, characterized by the wave number ($k$) dependence of the mean squared…

Developing new methods for the accurate and efficient calculations of real-time quantum correlation functions is deemed one of the most challenging problems of modern condensed matter theory. Many popular methods, such as centroid molecular…

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…

We investigate instability and reversibility within Hybrid Monte Carlo simulations using a non-perturbatively improved Wilson action. We demonstrate the onset of instability as tolerance parameters and molecular dynamics step sizes are…

The particle contact model is important for powder simulations. Although several contact models have been proposed, their validity has not yet been well established. Therefore, we perform molecular dynamics (MD) simulations to clarify the…

We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…

There is ample experimental evidence on the existence of several crystalline phases of C4F8, although they still have been not clearly identified. In this paper we perform a series of molecular dynamics (MD) simulations using a partially…

Calcein leakage assays are a standard experimental set-up for probing the extent of damage induced by external agents on synthetic lipid vesicles. The fluorescence signal associated with calcein release from liposomes is the signature of…

Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…

Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…

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…