Accurate Estimation of Solvation Free Energy Using Polynomial Fitting Techniques

作者：Shyu Conrad; Ytreberg F Marty^*

来源：Journal of Computational Chemistry, 2011, 32(1): 134-141.

DOI：10.1002/jcc.21609

• thermodynamic integration
• polynomial interpolation
• newton polynomial
• lagrange polynomial
• solvation free energy
• molecular dynamics

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 lambda) 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 lambda 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 lambda values, improve the accuracy for Delta F estimates without demanding additional simulations. We also provide general guidelines for use of polynomial fitting to estimate free energy. To allow researchers to immediately utilize these methods, free software and documentation is provided via http://www.phys.uidaho.edu/ytreberg/software.

• 出版日期2011-1-15