Binding free - energy calculation of ethanol on protein lush in water by molecular dynamics

Abstract

The paper deals with molecular dynamics for calculation of binding free - energy of ethanol on protein LUSH in water by GROMACS software and following the Dillgroup calculation procedure. The authors calculated the free energy for turning off the Lennard-Jones interactions of ethanol represented with the OPLS-AA force field in TIP3P water model. They achieved a high degree of statistical precision in molecular dynamic simulations, and by thermodynamic intergration method, the deviation of calculated free energy of ethanol hydration was about 0.02-0.60 kcal/mol from the experimental hydration free energy measurements. The calculated binding free energy of ethanol on protein LUSH in water is in a reasonable correspondence with experimental data.