Iranian Journal of Physics Research

Comparison of the thermodynamic integration and free energy perturbation in the computing alchemical free energy difference

Document Type : Original Article

Authors

Najla Hosseini 1
Mohammad Reza Ejtehadi 2

1 PhD student at Sharif University of Technology

2 Department of Physics, Sharif University of Technology

https://doi.org/10.47176/ijpr.22.2.81299
Abstract
On an atomistic scale, free energy calculations are important for our understanding of biological processes, which provides an insight to grasp the various mechanisms. Over the years, many computational methods have been developed to calculate free energy differences such as geometrical (e.g. umbrella sampling) and alchemical methods. In this work, we present alchemical-free energy methods, thermodynamic integration (TI) and free energy perturbation (FEP), to investigate polarization effect of paclitaxel drug. Then, we have compared our simulation studies using TI, FEP, and Hamiltonian replica exchange FEP from the perspective of computational cost and accuracy.

Keywords

Free energy difference "
" Molecular dynamics simulation "
" Free energy perturbation "
" Thermodynamic integration "
" Solvation free energy
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