Related papers: Single-Sweep Methods for Free Energy Calculations
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
The free energy landscapes of several fundamental processes are characterized by high barriers separating long-lived metastable states. In order to explore these type of landscapes enhanced sampling methods are used. While many such methods…
We introduce a straightforward, single-ensemble, path sampling approach to calculate free energy differences based on Jarzynski's relation. For a two-dimensional ``toy'' test system, the new (minimally optimized) method performs roughly one…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
We introduce a new method to simulate the physics of rare events. The method, an extension of the Temperature Accelerated Molecular Dynamics, comes in use when the collective variables introduced to characterize the rare events are either…
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, existing methods still face key limitations: classical…
We introduce an efficient and robust method to compute alchemical free energy differences, resulting from the application of multiple walker Adaptive Biasing Force (ABF) in conjunction with strongly damped Langevin $\lambda$-dynamics.…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
We demonstrate the application of artificial neural network (ANN) models to reverse Monte Carlo based thermodynamic calculations. Adsorption isotherms are generated for 2D square and triangular lattices. These lattices are considered…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
Experimental determination of absolute surface energies remains a challenge. We propose a simple method based on two independent measurements on 3D and 2D equilibrium shapes completed by the analysis of the thermal fluctuation of an…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
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…
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational cost of multidimensional sampling. In this work, we extend…
Enhanced sampling and free energy calculation algorithms of the Thermodynamic Integration family (such as the Adaptive Biasing Force method, ABF) are not based on the direct computation of a free energy surface, but rather of its gradient.…
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is…
We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway…
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is…
Massless scalar electrodynamics is studied at high temperature and zero chemical potential. I derive the free energy to order $\lambda^2$, $\lambda e^2$ and $e^4$ by effective field theory methods. The first step consists of the…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…