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High Performance Computing in Science and Engineering '09 pp 165–176Cite as

Development of Models for Large Molecules and Electrolytes in Solution for Process Engineering

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Abstract

Two of the most challenging tasks in molecular dynamics simulation are the simulation of long-range interactions like in electrolyte solutions and the internal degrees of freedom like in hydrogels. Both tasks lead to time consuming simulations with big systems. Therefore, massively parallel high performance computers are needed for both tasks. The first step of the present work was to test and validate different force fields for electrolyte solutions and hydrogels.

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References

  1. G. Bussi, D. Donadio, and M. Parrinello. Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126:014101, 2007.

    Article  Google Scholar 

  2. H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma. The missing term in effective pair potentials. Journal Of Physical Chemistry, 91:6269–6271, 1987.

    Article  Google Scholar 

  3. P. B. Balbuena, K. P. Johnston, and P. J. Rossky. Molecular dynamics simulation of electrolyte solutions in ambient and supercritical water. 1. Ion solvation. Journal of Physical Chemistry, 100:2706–2715, 1996.

    Article  Google Scholar 

  4. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81:3684–3690, 1984.

    Article  Google Scholar 

  5. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. Intermolecular Forces. D. Reidel Publishing Company, 1981.

    Google Scholar 

  6. L. X. Dang and T. M. Chang. Molecular mechanism of ion binding to the liquid/vapor interface of water. Journal of Physical Chemistry B, 106:235–238, 2002.

    Article  Google Scholar 

  7. T. Darden, D. York, and L. Pedersen. Particle mesh ewald - an n.log(n) method for ewald sums in large systems. Journal of Chemical Physics, 98:10089–10092, 1993.

    Article  Google Scholar 

  8. J. W. Eastwood, R. W. Hockney, and D. N. Lawrence. P3m3dp - the 3-dimensional periodic particle-particle-particle-mesh program. Computer Physics Communications, 19:215–261, 1980.

    Article  Google Scholar 

  9. P. P. Ewald. The calculation of optical and electrostatic grid potential. Annalen der Physik, 64:253–287, 1921.

    Article  Google Scholar 

  10. F. G. Fumi and M. P. Tosi. Ionic sizes + born repulsive parameters in nacl-type alkali halides. I. Huggins-Mayer + Pauling forms. Journal of Physics and Chemistry of Solids, 25:31–44, 1964.

    Article  Google Scholar 

  11. M. Heskins and J. E. Guillet. Solution properties of poly(n-isopropylacrylamide). Journal of Macromolecular Science, Part A, 8:1441–1455, 1968.

    Article  Google Scholar 

  12. B. Hess, C. Holm, and N. van der Vegt. Osmotic coefficients of atomistic nacl (aq) force fields. Journal of Chemical Physics, 124:164509, 2006.

    Article  Google Scholar 

  13. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4:435–447, 2008.

    Article  Google Scholar 

  14. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79:926–935, 1983.

    Article  Google Scholar 

  15. K. P. Jensen and W. L. Jorgensen. Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions. Journal of Chemical Theory and Computation, 2:1499–1509, 2006.

    Article  Google Scholar 

  16. W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. Journal of American Chemical Society, 118:11225–11236, 1996.

    Article  Google Scholar 

  17. W. L. Jorgensen and J. Tirado-Rives. The opls potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110:1657–1666, 1988.

    Article  Google Scholar 

  18. A. V. Lyulin, B. Dünweg, O. V. Borisov, and A. A. Darinskii. Computer simulation studies of a single polyelectrolyte chain in poor solvent. Macromolecules, 32:3264–3278, 1999.

    Article  Google Scholar 

  19. H. J. Limbach and C. Holm. Single-chain properties of polyelectrolytes in poor solvent. Journal of Physical Chemistry B, 107:8041–8055, 2003.

    Article  Google Scholar 

  20. P. J. Lenart, A. Jusufi, and A. Z. Panagiotopoulos. Effective potentials for 1 : 1 electrolyte solutions incorporating dielectric saturation and repulsive hydration. Journal of Chemical Physics, 126:044509, 2007.

    Article  Google Scholar 

  21. G. Longhi, F. Lebon, S. Abbate, and S. L. Fornili. Molecular dynamics simulation of a model oligomer for poly(n-isopropylamide) in water. Chemical Physics Letters, 386:123–127, 2004.

    Article  Google Scholar 

  22. B. A. Mann, K. Kremer, and C. Holm. The swelling behavior of charged hydrogels. Macromolecular Symposium, 237:90–107, 2006.

    Article  Google Scholar 

  23. F. Müller-Plathe and W. F. van Gunsteren. Solvation of poly(vinylalcohol) in water, ethanol and an equimolar water-ethanol mixture: structure and dynamics studied by molecular dynamics simulation. Polymer, 38/9:2259–2268, 1997.

    Article  Google Scholar 

  24. P. A. Netz and T. Dorfmüller. Computer simulation studies on the polymer-induced modification of water properities in polyacrylamide hydrogels. Journal of Physical Chemistry B, 102:4875–4886, 1998.

    Article  Google Scholar 

  25. B. Nick and U. W. Suter. Solubility of water in polymers - atomistic simulations. Computational and Theoretical Polymer Science, 11:49–55, 2001.

    Article  Google Scholar 

  26. N. A. Peppas, P. Bures, W. Leobandung, and H. Ichikawa. Hydrogels in pharmaceutical formulations. European Journal of Pharmaceutics and Biopharmaceutics, 50:27–46, 2000.

    Article  Google Scholar 

  27. B. G. Rao and U. C. Singh. A free-energy perturbation study of solvation in methanol and dimethyl-sulfoxide. Journal of the American Chemical Society, 112:3803–3811, 1990.

    Article  Google Scholar 

  28. T. P. Straatsma and H. J. C. Berendsen. Free-energy of ionic hydration - analysis of a thermodynamic integration technique to evaluate free-energy differences by molecular-dynamics simulations. Journal of Chemical Physics, 89:5876–5886, 1988.

    Article  Google Scholar 

  29. Y. Tamai, H. Tanaka, and K. Nakanishi. Molecular dynamics study of water in hydrogels. Molecular Simulation, 16:359–374 1996.

    Article  Google Scholar 

  30. H. van der Linden, W. Olthuis, and P. Bergveld. An efficient method for the fabrication of temperature-sensitive hydrogel microactuators. Lab on a Chip - Miniaturisation for Chemistry and Biology, 4:619–624, 2004.

    Article  Google Scholar 

  31. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen. Gromacs: Fast, flexible, and free. Journal of Computational Chemistry, 26:1701–1718, 2005.

    Article  Google Scholar 

  32. W. F. van Gunsteren and H. J. C. Berendsen. Gromos-87 manual. Biomos BV Nijenborgh 4, 9747 AG Groningen, The Netherlands, 1987.

    Google Scholar 

  33. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi. Biomolecular Simulation: The Gromos 96 Manual and User Guide. vdf Hochschulverlag AG an der ETH Zürich, Zürich, Switzerland, 1996.

    Google Scholar 

  34. D. R. Wheeler and J. Newman. Molecular dynamics simulations of multicomponent diffusion. 1. Equilibrium method. Journal of Physical Chemistry B, 108:18353–18361, 2004.

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663, Kaiserslautern, Germany

    Jonathan Walter

Authors
  1. Jonathan Walter
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  2. Stephan Deublein
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  3. Jadran Vrabec
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  4. Hans Hasse
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Corresponding author

Correspondence to Jonathan Walter .

Editor information

Editors and Affiliations

  1. Zentrum für Informationsdienste und, Hochleistungsrechnen (ZIH), TU Dresden, Dresden, 01062, Germany

    Wolfgang E. Nagel

  2. Abt. Angewandte Mathematik, Universität Freiburg, Hermann-Herder-Str. 10, Freiburg, 79104, Germany

    Dietmar B. Kröner

  3. Höchstleistungsrechenzentrum (HLRS), Universität Stuttgart, Nobelstr. 19, Stuttgart, 70569, Germany

    Michael M. Resch

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Walter, J., Deublein, S., Vrabec, J., Hasse, H. (2010). Development of Models for Large Molecules and Electrolytes in Solution for Process Engineering. In: Nagel, W., Kröner, D., Resch, M. (eds) High Performance Computing in Science and Engineering '09. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04665-0_12

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