Related papers: Free Energy Computation by Monte Carlo Integration
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…
We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from…
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…
Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We present a history-dependent Monte Carlo scheme for the efficient calculation of the free-energy of quantum systems, inspired by the Wang-Landau sampling and metadynamics method. When embedded in a path integral formulation, it is of…
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo…
We carry out highly accurate \emph{ab initio} path integral Monte Carlo (PIMC) simulations to directly estimate the free energy of various warm dense matter systems including the uniform electron gas and hydrogen without any nodal…
In this paper, I investigate more closely the recently proposed Free Energy Monte Carlo algorithm that is devised in particular for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest…
Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal…
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…
Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
We present an efficient Monte-Carlo method for long-range interacting systems to calculate free energy as a function of an order parameter. In this method, a variant of the Wang-Landau method regarding the order parameter is combined with…
The interfacial free energy between a crystal and a fluid, {\gamma} cf, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring {\gamma} cf experimentally, computer…
While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte…
We propose a new approach, "structure integration", enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
Markov chain Monte Carlo methods are primarily used for sampling from a given probability distribution and estimating multi-dimensional integrals based on the information contained in the generated samples. Whenever it is possible, more…