Related papers: Free Energy Computation by Monte Carlo Integration
Free energy as a function of polarization is calculated for the square-lattice $J_1$-$J_2$ Ising model for $J_2 < |J_1|/2$ using the random local field approximation (RLFA) and Monte Carlo (MC) simulations. Within RLFA, it reveals a…
From the onset of fundamental statistical mechanical constructs formulated in the late 19th century, alchemical free-energy methods slowly emerged and transitioned to become operational tools of biomolecular simulation applicable to a wide…
DL_MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation.…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
Using a thermodynamic integration scheme, we compute the free energy cost per unit area, $\gamma$, of forming an interface between a crystal and a frozen structured wall, formed by particles frozen into the same equilibrium structure as the…
Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying…
We present a unique derivation of metadynamics. The starting point for the derivation is an on-the-fly reweighting scheme but through an approximation we recover the standard metadynamics and the well-tempered metadynamics in a general form…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
We describe a novel method to obtain thermodynamic properties of quantum systems using Baysian Inference -- Maximum Entropy techniques. The method is applicable to energy values sampled at a discrete set of temperatures from Quantum Monte…
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
We discuss a computationally efficient classical many-body potential designed to model the Al-Al interaction in a wide range of bonding geometries. We show that the potential yields results in properties in excellent agreement with…
The computational modelling of reactions is simple in theory but can be quite tricky in practice. This article aims at the purpose of providing an assistance to a proper way of describing reactions theoretically and provides rough…
We present a direct calculation by molecular-dynamics computer simulation of the crystal/melt interfacial free energy, $\gamma$, for a system of hard spheres of diameter $\sigma$. The calculation is performed by thermodynamic integration…
We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction…
The microscopic approach to calculating the free energy of a three-dimensional Ising-like system in a homogeneous external field is developed in the higher non-Gaussian approximation (the $\rho^6$ model) at temperatures above the critical…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
The basic thermodynamic quantities for a non-interacting scalar field in a periodic potential composed of either a one-dimensional chain of Dirac $\delta$-$\delta^\prime$ functions or a specific potential with extended compact support are…
Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. The Coulomb interactions are emulated by harmonic repulsive forces, the force constants being…
With our recently proposed effective Hamiltonian via Monte Carlo, we are able to compute low energy physics of quantum systems. The advantage is that we can obtain not only the spectrum of ground and excited states, but also wave functions.…