Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics. These methods use a variable temperature or pressure that is updated on the fly in the thermodynamic controller. These methods are illustrated on a Lennard-Jones...

Using the Lennard-Jones (12-6) potential, a new equation of state is obtained that can predict properties of both gases and liquids relatively well. This equation of state is given as (Z-a)V2=(A/V2)-B, where Z is the compressibility factor, A and B are constants, and a is an adjustable parameter that depends on the temperature, volume and the nature of the fluid, and i...

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach ...

Holly E Holmes, Frances Wiseman, James M O'Callaghan, Jack A Wells, Victor LJ Tybulewicz, Elizabeth MC Fisher, and Mark F Lythgoe Centre for Advanced Biomedical Imaging, University College London, London, Greater London, United Kingdom, Department of Neurodegenerative Disease, Institute of Neurology, London, Greater London, United Kingdom, MRC National Institute for Medical Research, London, Gr...

The Gibbs ensemble Monte Carlo simulation is used to investigate the vapor–liquid phase behavior of a binary Lennard–Jonesmixture confined in a slit-like pore at reduced temperature T* = 1.0. Our simulation program is tested by comparing the simulated phase diagram with the previous simulation results from various methods. Then phase diagrams of a binary asymmetric Lennard–Jones mixture confine...

Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy functions using data various origin. Our allows propagating uncertainty finite trajectories to automatically performing with respect simulation parameters. Furthe...