相关论文: Discretization errors in molecular dynamics simula…

We simulate TIP4P/2005 water in the temperature range of 257 K to 318 K with time-steps $\delta =$ 0.25, 0.50, 2.00, and 4.00 fs. The density-temperature behavior obtained using 0.25 or 0.50 fs are in excellent agreement with each other but…

Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical…

The so-called thermodynamic anomalies of water form an integral part of the peculiar behaviour of this both important and ubiquitous molecule. In this paper our aim is to establish whether the recently proposed TIP4P/2005 model is capable…

We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we establish how these errors depend on Mach number, Knudsen number, number of…

We simulate TIP3P water using a constrained Monte Carlo algorithm to generate electrostatic interactions eliminating the need to sum over long ranged Coulomb interactions. We study discretization errors when interpolating charges using…

We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…

The model Tip4p/{\epsilon} for water is tested for the presence of thermodynamic and dy- namic anomalies. Molecular dynamic simulations for this model were performed and we show that for this system the density versus temperature at…

In this paper we introduce adaptive time step control for simulation of evolution of ice sheets. The discretization error in the approximations is estimated using "Milne's device" by comparing the result from two different methods in a…

We study numerical methods for sampling probability measures in high dimension where the underlying model is only approximately identified with a gradient system. Extended stochastic dynamical methods are discussed which have application to…

We investigate the temperature dependence of thermodynamic (density, isobaric heat capacity), dynamical (self-diffusion coefficient, shear viscosity), and dielectric properties of several water models, the commonly employed TIP3P water…

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…

With the objective of demonstrating usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition.…

We review and compare numerical methods that simultaneously control temperature while preserving the momentum, a family of particle simulation methods commonly used for the modelling of complex fluids and polymers. The class of methods…

Many complex fluids can be described by continuum hydrodynamic field equations, to which noise must be added in order to capture thermal fluctuations. In almost all cases, the resulting coarse-grained stochastic partial differential…

A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…

We propose a novel discrete Poisson equation approach to estimate the statistical error of a broad class of numerical integrators for the underdamped Langevin dynamics. The statistical error refers to the mean square error of the estimator…

Reliable dynamical properties from molecular dynamics simulations require careful control of thermostatting artifacts. We systematically assess how NVE, deterministic thermostats, velocity-rescale dynamics, and stochastic Langevin-type…

In the last decades a large effort has been devoted to the study of water confined in hydrophobic geometries at the nanoscale (tubes, slit pores), because of the multiple technological applications of such systems, ranging from drugs…

Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…

In this work, the uncertainties in the dielectric constants of polar liquids, computed using molecular dynamics (MD) simulations, are compared for two different calculations schemes. Expressions of the uncertainty are derived for the…