Related Experiment Video
Updated: Jul 13, 2026

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
Published on: September 17, 2021
Absolute free-energy calculations of liquids using a harmonic reference state
Michael D Tyka1, Richard B Sessions, Anthony R Clarke
1Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, UK. mtyka@u.washington.edu
Abstract:
Absolute free-energy methods provide a potential solution to the overlap problem in free-energy calculations. In this paper, we report an extension of the previously published confinement method (J. Phys. Chem. B 2006, 110, 17212-20) to fluid simulations. Absolute free energies of liquid argon and liquid water are obtained accurately and compared with results from thermodynamic integration. The method works by transforming the liquid state into a harmonic, solid reference state. This is achieved using a special restraint potential that allows molecules to change their restraint position during the simulation, which circumvents the need for the molecules to sample the full extent of their translational freedom. The absolute free energy of the completely restrained reference state is obtained from a normal mode calculation. Because of the generic reference state used, the method is applicable to nonhomogeneous, diffusive systems and could provide an alternative method in situations in which solute annihilation fails due to the size of the solute. Potential applications include calculation of solvation energies of large molecules and free energies of peptide conformational changes in explicit solvent.
Related Concept Videos
Calculating Standard Free Energy Changes
Gibbs Free Energy
Thermodynamic Properties of Ideal Solutions
Calculation of First-Law Quantities II
Third Law of Thermodynamics
Enthalpy of Solution

