Related papers: Bounding free energy difference with flow matching
The methodology based on the association of the Variational Method with Supersymmetric Quantum Mechanics is used to evaluate the energy states of the confined hydrogen atom.
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…
The free energy balance equation for gyrokinetic fluctuations is derived and applied to instabilities. An additional term due to electromagnetic sources is included. This can provide a simpler way to compute the free energy balance in…
A generalization of the free energy perturbation identity is derived, and a computational strategy based on this result is presented. A simple example illustrates the efficiency gains that can be achieved with this method.
Several research groups have recently reported {\em ab initio} calculations of the melting properties of metals based on density functional theory, but there have been unexpectedly large disagreements between results obtained by different…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
A free energy landscape estimation-method based on Bayesian inference is presented and used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics, where the simulations are carried…
A variational approach for the free energy is used to study the three-dimensional anisotropic XY model in the presence of a crystal field. The magnetization and the phase diagrams as a function of the parameters of the Hamiltonian are…
In the case of a large class of static spherically symmetric black hole solutions in higher order modified gravity models, an expression for the associated energy is proposed and identified as a quantity proportional to the constant of…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
In this work, we consider the problem of training a generator from evaluations of energy functions or unnormalized densities. This is a fundamental problem in probabilistic inference, which is crucial for scientific applications such as…
We describe a variational procedure for calculating the energy of an electron gas in which the long-range Coulomb interaction is truncated by the screening effect of a nearby metallic gate. We use this procedure to compute the quantum…
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…
The expression of the free energy of a liquid in terms of an explicit decomposition of the particle configurations into local coordination clusters is examined. We argue that the major contribution to the entropy associated with structural…
Approximate formulas are derived to describe energy loss in a harmonic oscillator that experiences three distinct damping mechanisms: constant-magnitude (Coulomb), velocity-proportional (Stokes), and velocity-squared (Newton), using…
Nonequilibrium, ``fast switching'' estimates of equilibrium free energy differences, Delta F, are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced…
We analytically obtain the free energy and thermodynamic geometry of holographic superconductors in $2+1$-dimensions. The gravitational theory in the bulk dual to this $2+1$-dimensional strongly coupled theory lives in the $3+1$-dimensions…