Related papers: Bounding free energy difference with flow matching
Free energy calculations are widely used tools in computational chemistry, but their dependence on the assignment of partial charges during force field parametrization reduces their accuracy and reproducibility. In this work, we highlight…
The Helmholtz free-energy W is calculated as a function of separation distance for two molecules in a fluid, A and B, whose mutual interaction is described by a spherically symmetric potential. For the equilibrium A + B = AB occurring in a…
A compressed knotted ring polymer in a confining cavity is modelled by a knotted lattice polygon confined in a cube in ${\mathbb Z}^3$. The GAS algorithm [17] is used to sample lattice polygons of fixed knot type in a confining cube and to…
A novel error measure, referred to as the hysteresis error, is developed from the Crooks fluctuation theorem to evaluate sampling quality in free energy calculations. Theory and numerical free energy of hydration calculations are used to…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
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 critical behavior of a 3D Ising-like system is studied at the microscopic level of consideration. The free energy of ordering is calculated analytically as an explicit function of temperature, an external field and the initial…
We develop a fluctuation framework to quantify the free energy difference between two equilibrium states connected by nonequilibrium processes under arbitrary dynamics and system-environment coupling. For an open system described by the…
One may impose to a system with spontaneous broken symmetry, boundary conditions which correspond to different pure states at two ends of a sample. For a discrete Ising-like broken symmetry, boundary conditions with opposite spins in two…
We introduce a simulation technique to compute the free energy difference between two hydrate structures of different stoichiometry connected to a reservoir of gas molecules at a prescribed pressure. The method permits the determination of…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
Active nematics are influenced by alignment angle singularities called topological defects. The localization of these defects is of major interest for biological applications. The total distortion of alignment angles due to defects is…
Estimating free energy differences, an important problem in computational drug discovery and in a wide range of other application areas, commonly involves a computationally intensive process of sampling a family of high-dimensional…
We study a determinantal Coulomb gas in the complex plane associated with the external potential $$ Q(z)=\frac{1}{1-\tau^2}\big(|z|^2-\tau \text{Re } z^2\big)-2c\log|z-a|, $$ where $\tau\in[0,1)$, $c\ge0$, and $a\ge0$. In the regimes where…
The free energy and other thermodynamic properties of hexagonal-close-packed iron are calculated by direct {\em ab initio} methods over a wide range of pressures and temperatures relevant to the Earth's core. The {\em ab initio}…
We study the dynamics of an interacting classical gas trapped in a double-well potential at finite temperature. Two model potentials are considered: a cubic box with a square barrier in the middle, and a harmonic trap with a gaussian…
In this work, we propose two models of coupled harmonic oscillators under Brownian motion to computationally study the applications of fluctuation theorems. This paper also illustrates how to analytically calculate free energy differences…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
We develop a rigorous error analysis for coarse-graining of defect-formation free energy. For a one-dimensional constrained atomistic system, we establish the thermodynamic limit of the defect-formation free energy and obtain explicitly the…