Related papers: Nonequilibrium free-energy calculation of solids u…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
An alternative approach - nonequilibrium evolution thermodynamics, is compared with classical Landau approach. A statistical justification of the approach is carried out with help of probability distribution function on an example of a…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…
A simple, efficient, and accurate method is proposed to map multi-dimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [Maragliano & Vanden-Eijnden, Chem. Phys. Lett. 426,…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
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…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
This paper presents a load balancing strategy for reaction rate evaluation and chemistry integration in reacting flow simulations. The large disparity in scales during combustion introduces stiffness in the numerical integration of the PDEs…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
Predictions of relative stabilities of (competing) molecular crystals are of great technological relevance, most notably for the pharmaceutical industry. However, they present a long-standing challenge for modeling, as often minuscule free…
This report presents the application of polynomial regression for estimating free energy differences using thermodynamic integration. We employ linear regression to construct a polynomial that optimally fits the thermodynamic integration…
We present a new approach to analyze homogeneous nucleation based on non-equilibrium thermodynamics. The starting point is the formulation of a Gibbs equation for the variations of the entropy of the system, whose state is characterized by…
Obtaining the free energy of large molecules from quantum mechanical energy functions is a longstanding challenge. We describe a method that allows us to estimate, at the quantum mechanical level, the harmonic contributions to the…
Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach,…
We combine the formalisms of diagonal entropy and Jarzynski Equality to study the thermodynamic properties of closed quantum systems. Applying this approach to a quantum harmonic oscillator, the diagonal entropy offers a notion of…
A new mathematical model for non-equilibrium evaporation/condensation including boiling effect is proposed. A simplified differential-algebraic system of equations is obtained. A code to solve numerically this differential-algebraic system…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…