Related papers: Free energy calculations of a proton transfer reac…
We study the kinetics of crystallization in deeply supercooled liquid silicon employing computer simulations and the Stillinger-Weber three body potential. The free energy barriers to crystallisation are computed using umbrella sampling…
In this paper, we report dynamic Monte Carlo simulations of melting and crystallization in a single-chain system. Their free energy barriers are calculated by the umbrella sampling method and can be described well by a simple expression…
First principles calculations based on density functional theory, with generalised gradient corrections and ultrasoft pseudopotentials, have been used to simulate solid and liquid aluminium in direct coexistence at zero pressure.…
We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters…
First steps towards developing a new perturbation theory for molecular liquids are taken. By choosing a new form of splitting the site-site potential functions between molecules, we will get a set of atomic fluids as the reference system…
We study the dynamics of parallel tempering simulations, also known as the replica exchange technique, which has become the method of choice for simulation of proteins and other complex systems. Recent results for the optimal choice of the…
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
Simulation of warm dense matter requires computational methods that capture both quantum and classical behavior efficiently under high-temperature, high-density conditions. Currently, density functional theory molecular dynamics is used to…
Multistate empirical valence bond (EVB) models provide an accurate description of the energetics of proton transfer and solvation in complex molecular systems and can be efficiently used in molecular dynamics computer simulations. Within…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
We propose a method, Temperature Integration, which allows an efficient calculation of free energy differences between two systems of interest, with the same degrees of freedom, which may have rough energy landscapes. The method is based on…
First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing…
{\em Ab initio} techniques based on density functional theory in the projector-augmented-wave implementation are used to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and…
The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights which often demand involving and time consuming calculations. Here…
We report a novel Monte Carlo scheme that greatly enhances the power of parallel-tempering simulations. In this method, we boost the accumulation of statistical averages by including information about all potential parallel tempering trial…
Free energy calculations of two crystalline phases of the molecular compound S8 were performed via molecular dynamics simulations of these crystals. The elemental sulphur S8 molecule model used in our MD calculations consists of a…
The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterization of such free…
Free energy sampling methods allow studying the full dynamics of activated processes. Unfortunately, the affordable accuracy of the potential describing the energy and forces of the system is usually rather low. Here we introduce a new…
In molecular simulations, machine-learning force fields can achieve ab initio accuracy at a lower cost but remain limited in the explicit modeling of electrons. In this work, we develop an electron-aware machine-learning force field, in…