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

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Hosseini Najla; Ejtehadi Mohammad Reza

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Journal Paper

Paper Information

Journal: Iranian Journal of Physics Research Year:2022 | Volume:22 | Issue:2 (پیاپی 88) Page(s): 315-325

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Information Journal Paper

Title

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

Author(s)

Hosseini Najla | Ejtehadi Mohammad Reza | Issue Writer Certificate

Keywords

Free energy differenceQ4

Molecular dynamics simulationQ4

Free energy perturbationQ4

Thermodynamic integrationQ4

Solvation free energyQ4

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.

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