Accurate estimation of solvation free energy using polynomial fitting techniques.

Journal of Computational Chemistry
Conrad Shyu, F Marty Ytreberg

Abstract

This report details an approach to improve the accuracy of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable λ) and its application to calculating solvation free energy. The central idea is to utilize polynomial fitting schemes to approximate the thermodynamic integration data to improve the accuracy of the free energy difference estimates. Previously, we introduced the use of polynomial regression technique to fit thermodynamic integration data (Shyu and Ytreberg, J Comput Chem, 2009, 30, 2297). In this report we introduce polynomial and spline interpolation techniques. Two systems with analytically solvable relative free energies are used to test the accuracy of the interpolation approach. We also use both interpolation and regression methods to determine a small molecule solvation free energy. Our simulations show that, using such polynomial techniques and nonequidistant λ values, the solvation free energy can be estimated with high accuracy without using soft-core scaling and separate simulations for Lennard-Jones and partial charges. The results from our study suggest that these polynomial techniques, especially with use of nonequidistant ...Continue Reading

References

Dec 1, 1989·Journal of Computer-aided Molecular Design·M P Allen, M R Wilson
Mar 12, 1988·Lancet·P HelminenL Peltonen
Nov 23, 2006·The Journal of Chemical Physics·F Marty YtrebergDaniel M Zuckerman
Dec 11, 2007·The Journal of Chemical Physics·Thomas SteinbrecherDavid A Case

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Citations

Nov 16, 2010·Toxicology and Applied Pharmacology·Conrad ShyuF Marty Ytreberg
Jul 22, 2014·Evidence-based Complementary and Alternative Medicine : ECAM·WooSang JungKiHo Cho
Sep 29, 2011·Journal of Computational Chemistry·Floris P Buelens, Helmut Grubmüller
Mar 2, 2019·Journal of Chemical Theory and Computation·David F Hahn, Philippe H Hünenberger
Aug 17, 2020·Journal of Chemical Information and Modeling·Gerhard KönigSereina Riniker
Jan 23, 2018·Journal of Chemical Theory and Computation·Timothy J Giese, Darrin M York

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