Assimilating Radial Distribution Functions To Build Water Models with Improved Structural Properties

The structural properties of three- and four-site water models are improved by extending the ForceBalance parametrization code to include a new methodology allowing for the targeting of any radial distribution function (RDF) during the parametrization of a force field. The mean squared difference (MSD) between the experimental and simulated RDFs contributes to an objective function, allowing for the systematic optimization of force field parameters to reach closer overall agreement with experiment. RDF fitting is applied to develop modified versions of the TIP3P and TIP4P/2005 water models in which the Lennard-Jones potential is replaced by a Buckingham potential. The optimized TIP3P-Buckingham and TIP4P-Buckingham potentials feature 93 and 98% lower MSDs in the OO RDF compared to the TIP3P and TIP4P/2005 models respectively, with marked decreases in the height of the first peak. Additionally, these Buckingham models predict the entropy of water more accurately, reducing the error in the entropy of TIP3P from 11 to 3% and the error in the entropy of TIP4P/2005 from 11 to 2%. These new Buckingham models have improved predictive power for many nonfitted properties particularly in the case of TIP3P. Our work directly demonstrates how the Buckingham potential can improve the description of water's structural properties beyond the Lennard-Jones potential. Moreover, adding a Buckingham potential is a favorable alternative to adding interaction sites in terms of computational speed on modern GPU hardware.

[1]  Diwakar Shukla,et al.  OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. , 2013, Journal of chemical theory and computation.

[2]  Vijay S Pande,et al.  Building Force Fields: An Automatic, Systematic, and Reproducible Approach. , 2014, The journal of physical chemistry letters.

[3]  Pengyu Y. Ren,et al.  United polarizable multipole water model for molecular mechanics simulation. , 2015, The Journal of chemical physics.

[4]  Alan K. Soper,et al.  The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa , 2000 .

[5]  Michael R. Shirts,et al.  Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. , 2011, The Journal of chemical physics.

[6]  T. Ichiye,et al.  Temperature and pressure dependence of the optimized soft-sticky dipole-quadrupole-octupole water model. , 2010, The Journal of chemical physics.

[7]  William L. Jorgensen,et al.  Temperature and size dependence for Monte Carlo simulations of TIP4P water , 1985 .

[8]  C. Vega,et al.  A potential model for the study of ices and amorphous water: TIP4P/Ice. , 2005, The Journal of chemical physics.

[9]  D. Huggins Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm. , 2014, Journal of chemical theory and computation.

[10]  Michael R. Shirts,et al.  Statistically optimal analysis of samples from multiple equilibrium states. , 2008, The Journal of chemical physics.

[11]  David J Huggins,et al.  Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models. , 2012, The Journal of chemical physics.

[12]  Lee-Ping Wang,et al.  Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data. , 2013, Journal of chemical theory and computation.

[13]  R. Buckingham The present status of intermolecular potentials for calculations of transport properties , 1961 .

[14]  J. D. Bernal,et al.  A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl Ions , 1933 .

[15]  B. Laird,et al.  Calculation of the entropy of binary hard sphere mixtures from pair correlation functions , 1992 .

[16]  Thomas J Lane,et al.  MDTraj: a modern, open library for the analysis of molecular dynamics trajectories , 2014, bioRxiv.

[17]  Saeed Izadi,et al.  Building Water Models: A Different Approach , 2014, The journal of physical chemistry letters.

[18]  Greg L. Hura,et al.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. , 2004, The Journal of chemical physics.

[19]  D. J. Price,et al.  A modified TIP3P water potential for simulation with Ewald summation. , 2004, The Journal of chemical physics.

[20]  G. Voth,et al.  Flexible simple point-charge water model with improved liquid-state properties. , 2006, The Journal of chemical physics.

[21]  W. L. Jorgensen Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water , 2002 .

[22]  Alexander D. MacKerell,et al.  A simple polarizable model of water based on classical Drude oscillators , 2003 .

[23]  Themis Lazaridis,et al.  Orientational correlations and entropy in liquid water , 1996 .

[24]  A. Soper Orientational correlation function for molecular liquids: The case of liquid water , 1994 .

[25]  S. Rick A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums. , 2004, The Journal of chemical physics.

[26]  D. Friend The International Association for the Properties of Water and Steam , 2009 .

[27]  David L. Mobley,et al.  Alchemical Free Energy Calculations : Ready for Prime Time ? , 2016 .

[28]  David J. Huggins,et al.  Benchmarking the thermodynamic analysis of water molecules around a model beta sheet , 2012, J. Comput. Chem..

[29]  S. Price,et al.  An overlap model for estimating the anisotropy of repulsion , 1990 .

[30]  R. Silver,et al.  Hydrogen-hydrogen pair correlation function in liquid water , 1982 .

[31]  Carlos Vega,et al.  Simulating water with rigid non-polarizable models: a general perspective. , 2011, Physical chemistry chemical physics : PCCP.

[32]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[33]  Pengyu Y. Ren,et al.  Systematic improvement of a classical molecular model of water. , 2013, The journal of physical chemistry. B.

[34]  J. Onuchic,et al.  Water mediation in protein folding and molecular recognition. , 2006, Annual review of biophysics and biomolecular structure.

[35]  M. Gilson,et al.  Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.

[36]  John E. Stone,et al.  Fast analysis of molecular dynamics trajectories with graphics processing units - Radial distribution function histogramming , 2011, J. Comput. Phys..

[37]  A. Soper,et al.  Joint structure refinement of x-ray and neutron diffraction data on disordered materials: application to liquid water , 2007, Journal of physics. Condensed matter : an Institute of Physics journal.