The accelerated weight histogram method for alchemical free energy calculations

20Citations
Citations of this article
40Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

The accelerated weight histogram method is an enhanced sampling technique used to explore free energy landscapes by applying an adaptive bias. The method is general and easy to extend. Herein, we show how it can be used to efficiently sample alchemical transformations, commonly used for, e.g., solvation and binding free energy calculations. We present calculations and convergence of the hydration free energy of testosterone, representing drug-like molecules. We also include methane and ethanol to validate the results. The protocol is easy to use, does not require a careful choice of parameters, and scales well to accessible resources, and the results converge at least as quickly as when using conventional methods. One benefit of the method is that it can easily be combined with other reaction coordinates, such as intermolecular distances.

References Powered by Scopus

Comparison of simple potential functions for simulating liquid water

34808Citations
N/AReaders
Get full text

Canonical dynamics: Equilibrium phase-space distributions

19391Citations
N/AReaders
Get full text

A smooth particle mesh Ewald method

18662Citations
N/AReaders
Get full text

Cited by Powered by Scopus

Best Practices in Constant pH MD Simulations: Accuracy and Sampling

32Citations
N/AReaders
Get full text

Skin permeability prediction with MD simulation sampling spatial and alchemical reaction coordinates

11Citations
N/AReaders
Get full text

Molecular structure, vibrational spectral, electron density analysis on linaloe oil and molecular docking efficacy against the therapeutic target on human immunodeficiency virus-1 organism (VIRAL protein)

11Citations
N/AReaders
Get full text

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Cite

CITATION STYLE

APA

Lundborg, M., Lidmar, J., & Hess, B. (2021). The accelerated weight histogram method for alchemical free energy calculations. Journal of Chemical Physics, 154(20). https://doi.org/10.1063/5.0044352

Readers' Seniority

Tooltip

Researcher 11

46%

PhD / Post grad / Masters / Doc 9

38%

Professor / Associate Prof. 3

13%

Lecturer / Post doc 1

4%

Readers' Discipline

Tooltip

Chemistry 9

43%

Biochemistry, Genetics and Molecular Bi... 5

24%

Physics and Astronomy 4

19%

Chemical Engineering 3

14%

Save time finding and organizing research with Mendeley

Sign up for free