Molecular dynamics simulations of aqueous ions at the liquid–vapor interface accelerated using graphics processors

Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large‐scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, scientists have returned to exploring the power of graphics processing units (GPUs) for various applications, such as MD, enabled by the recent advances in hardware and integrated programming interfaces such as NVIDIA's CUDA platform. One area of particular interest within the context of chemical applications is that of aqueous interfaces, the salt solutions of which have found application as model systems for studying atmospheric process as well as physical behaviors such as the Hoffmeister effect. Here, we present results of GPU‐accelerated simulations of the liquid–vapor interface of aqueous sodium iodide solutions. Analysis of various properties, such as density and surface tension, demonstrates that our model is consistent with previous studies of similar systems. In particular, we find that the current combination of water and ion force fields coupled with the ability to simulate surfaces of differing area enabled by GPU hardware is able to reproduce the experimental trend of increasing salt solution surface tension relative to pure water. In terms of performance, our GPU implementation performs equivalent to CHARMM running on 21 CPUs. Finally, we address possible issues with the accuracy of MD simulaions caused by nonstandard single‐precision arithmetic implemented on current GPUs. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011

[1]  Kyle A. Beauchamp,et al.  Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). , 2010, Journal of the American Chemical Society.

[2]  Michele Parrinello,et al.  Structural, electronic, and bonding properties of liquid water from first principles , 1999 .

[3]  Pavel Jungwirth,et al.  Specific ion effects at the air/water interface. , 2006, Chemical reviews.

[4]  Y. Levin,et al.  Ions at the air-water interface: an end to a hundred-year-old mystery? , 2009, Physical review letters.

[5]  W. Im,et al.  Theoretical and computational models of biological ion channels , 2004, Quarterly Reviews of Biophysics.

[6]  M J Harvey,et al.  An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. , 2009, Journal of chemical theory and computation.

[7]  Y. Levin Polarizable ions at interfaces. , 2008, Physical review letters.

[8]  Joshua A. Anderson,et al.  General purpose molecular dynamics simulations fully implemented on graphics processing units , 2008, J. Comput. Phys..

[9]  H. Allen,et al.  Vibrational Spectroscopy of Aqueous Sodium Halide Solutions and Air-Liquid Interfaces: Observation of Increased Interfacial Depth , 2004 .

[10]  Peter A. Kollman,et al.  Ion solvation in polarizable water: molecular dynamics simulations , 1991 .

[11]  M. Berkowitz,et al.  Many-body effects in molecular dynamics simulations of Na +(H2O)n and Cl-(H2O) n clusters , 1991 .

[12]  A. Arnold,et al.  Harvesting graphics power for MD simulations , 2007, 0709.3225.

[13]  Elizabeth A. Raymond,et al.  Probing the Molecular Structure and Bonding of the Surface of Aqueous Salt Solutions , 2004 .

[14]  Klaus Schulten,et al.  Accelerating Molecular Modeling Applications with GPU Computing , 2009 .

[15]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[16]  L. Dang,et al.  Recent advances in molecular simulations of ion solvation at liquid interfaces. , 2006, Chemical reviews.

[17]  B. Finlayson‐Pitts The tropospheric chemistry of sea salt: a molecular-level view of the chemistry of NaCl and NaBr. , 2003, Chemical reviews.

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

[19]  C. Brooks Computer simulation of liquids , 1989 .

[20]  Sandeep Patel,et al.  Comparison of the Solvation Structure of Polarizable and Nonpolarizable Ions in Bulk Water and Near the Aqueous Liquid-Vapor Interface , 2008 .

[21]  G. Hummer,et al.  Computer simulation of aqueous Na-Cl electrolytes , 1994 .

[22]  R. Saykally,et al.  Confirmation of enhanced anion concentration at the liquid water surface , 2004 .

[23]  Capillary waves at the liquid-vapor interface and the surface tension of water. , 2006, The Journal of chemical physics.

[24]  J. Perram,et al.  Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants , 1980, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[25]  Chris H. Q. Ding,et al.  Using accurate arithmetics to improve numerical reproducibility and stability in parallel applications , 2000, ICS '00.

[26]  Becky L. Eggimann,et al.  Size Effects on the Solvation of Anions at the Aqueous Liquid−Vapor Interface , 2008 .

[27]  B. Roux,et al.  Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field. , 2006, The journal of physical chemistry. B.

[28]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[29]  J. A. Barker,et al.  Monte Carlo studies of the dielectric properties of water-like models , 1973 .

[30]  Ilan Benjamin,et al.  Chemical Reactions and Solvation at Liquid Interfaces: A Microscopic Perspective. , 1996, Chemical reviews.

[31]  R. Unger,et al.  Chaos in protein dynamics , 1997, Proteins.

[32]  Yunfei Chen,et al.  GPU accelerated molecular dynamics simulation of thermal conductivities , 2007, J. Comput. Phys..

[33]  David H. Bailey,et al.  High-precision floating-point arithmetic in scientific computation , 2004, Computing in Science & Engineering.

[34]  M. Neumann The dielectric constant of water. Computer simulations with the MCY potential , 1985 .

[35]  G. Patey,et al.  Fluids of polarizable hard spheres with dipoles and tetrahedral quadrupoles Integral equation results with application to liquid water , 1982 .

[36]  J. Gibbs,et al.  The collected works of J. Willard Gibbs , 1948 .

[37]  B. N. Volkov,et al.  International Tables of the Surface Tension of Water , 1983 .

[38]  J. Ilja Siepmann,et al.  Development of Polarizable Water Force Fields for Phase Equilibrium Calculations , 2000 .

[39]  A. Garcia,et al.  Role of Backbone Hydration and Salt-Bridge Formation in Stability of α-Helix in Solution , 2003 .

[40]  D. Peter Tieleman,et al.  Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories , 2008, J. Comput. Chem..

[41]  D. Tobias,et al.  Propensity of soft ions for the air/water interface , 2004 .

[42]  M. Cordeiro,et al.  Quantum and simulation studies of X-(H2O)n systems , 1999 .

[43]  Michael L. Klein,et al.  Effective pair potentials and the properties of water , 1989 .

[44]  Vijay S. Pande,et al.  Accelerating molecular dynamic simulation on graphics processing units , 2009, J. Comput. Chem..

[45]  Philip Saponaro,et al.  Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs , 2010, 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS).

[46]  Hubert Nguyen,et al.  GPU Gems 3 , 2007 .