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QM/MM Simulation of the First Step of Vision

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High Performance Computing in Science and Engineering, Munich 2004

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References

  1. Wald, G. (1968) Science 162, 230.

    Google Scholar 

  2. Mathies, R.A., Lugtenburg, J. (2000) Handb. Biol. Phys. 3, 55

    Article  Google Scholar 

  3. Hellingwerf, K.J., Hoff, W.D., Crielaard, W. (1996) Molecular Microbiology 21, 683

    Article  Google Scholar 

  4. Birge, R.R. (1981) Ann. Rev. Biophys. Bioeng. 74, 5669

    Google Scholar 

  5. Du, P., Davidson, E.R. (1990) J. Phys. Chem. 94, 7013

    Article  Google Scholar 

  6. Vreven, T., Bernardi, F., Garavelli, M., Olivucci, M., Robb, M.A., Schlegel, H.B. (1997) J. Am. Chem. Soc. 119, 12687

    Article  Google Scholar 

  7. Garavelli, M., Celani, P., Bernardi, F., Robb, M.A., Olivucci, M. (1997) J. Am. Chem. Soc, 119, 6891

    Article  Google Scholar 

  8. Yamamoto, S., Wasada, H., Kakitani, K. (1998) J. Mol. Struct. (THEOCHEM) 451, 151

    Article  Google Scholar 

  9. Ben-Nun, M., Molnar, F., Schulten, K., Martinez, T.J. (2002) PNAS 99, 1769

    Article  Google Scholar 

  10. De Vico, L., Page, C.S., Garavelli, M., Bernardi, F., Basosi, R., Olivucci, M. (2002) J. Am. Chem. Soc. 124, 4124

    Article  Google Scholar 

  11. Schoenlein, R.W., Peteanu, L.A., Mathies, R.A., Shank, C.V. (1991) Science 254, 412

    Google Scholar 

  12. Kim, J.E., Tauber, M.J., Mathies, R.A. (2001) Biochemistry 40, 13774

    Article  Google Scholar 

  13. Liu, R.S.H., Browne, D.T. (1986) Acc. Chem. Res. 19, 42

    Article  Google Scholar 

  14. Warshel, A. (1976) Nature 260, 679

    Article  Google Scholar 

  15. Röhrig, U. F., Nonnenberg, C., Frank, I., Guidoni, L., Rothlisberger, U. in ”High Performance Computing in Science and Engineering 2002 — Transactions of the First Joint HLRB and KONWIHR Result and Reviewing Workshop”, Springer, 2002.

    Google Scholar 

  16. Röhrig, U., Guidoni, L., Rothlisberger, U. (2002) Biochemistry 41, 10799

    Article  Google Scholar 

  17. Teller, D.C., Okada, T., Behnke, C.A., Palczewski, K., Stenkamp, R.E. (2001) Biochemistry 40, 7761

    Article  Google Scholar 

  18. Frank, I., Hutter, J., Marx, D., Parrinello, M. (1998) J. Chem. Phys. 108, 4060

    Article  Google Scholar 

  19. Molteni, C., Frank, I., Parrinello, M. (1999) J. Am. Chem. Soc. 121, 12177

    Article  Google Scholar 

  20. Molteni, C., Frank, I., Parrinello, M. (2001) Comput. Mater. Science 20, 311

    Article  Google Scholar 

  21. Car, R., Parrinello, M. (1985) Phys. Rev. Lett. 55, 2471

    Article  Google Scholar 

  22. Parrinello, M. (1997) Solid State Commun. 102, 107

    Article  Google Scholar 

  23. Marx, D., Hutter, J. (2000): Ab Initio Molecular Dynamics: Theory and Implementation. In: Grotendorst, J. (ed) Modern Methods and Algorithms of Quantum Chemistry. Forschungszentrum Jülich, NIC Series. 1, 301

    Google Scholar 

  24. Hohenberg, P., Kohn, W. (1964) Phys. Rev. B 136, 864

    Article  MathSciNet  Google Scholar 

  25. Kohn, W., Sham, L.J. (1965) Phys. Rev. A 140, 1133

    Article  MathSciNet  Google Scholar 

  26. Parr, R.G., Yang, W. (1989): Density Functional Theory of Atoms and Molecules. Oxford University Press, Oxford

    Google Scholar 

  27. Dreizler, R.M., Gross, E.K.U. (1990): Density Functional Theory. Springer, Berlin

    MATH  Google Scholar 

  28. Becke, A.D. (1988) Phys. Rev. A 38, 3098

    Article  Google Scholar 

  29. Lee, C., Yang, W., Parr, R.G. (1988) Phys. Rev. B 37, 785

    Article  Google Scholar 

  30. Perdew, J.P., Zunger, A. (1981) Phys. Rev. B 23, 5048

    Article  Google Scholar 

  31. Wang, J., Cieplak, P. Kollman, P.A. (2000) J. Comput. Chem. 21, 1049

    Article  Google Scholar 

  32. Laio, A., VandeVondele, J., Rothlisberger, U. (2002) J. Chem. Phys. 116, 6941

    Article  Google Scholar 

  33. Laio, A., VandeVondele, J., Rothlisberger, U. (2002) J. Phys. Chem. B 106, 7300

    Article  Google Scholar 

  34. Röhrig, U. F., Frank, I., Hutter, J., Laio, A., VandeVondele, J., Rothlisberger, U. (2003) ChemPhysChem 4, 1177

    Article  Google Scholar 

  35. Goedecker, S., Umrigar, C.J. (1997) Phys. Rev. A 55, 1765

    Article  Google Scholar 

  36. Grimm, S., Nonnenberg, C., Frank, I. (2003) J. Chem. Phys. 119, 11574

    Article  Google Scholar 

  37. Hsu, C., Hirata, S., Head-Gordon, M. (2001) J. Phys. Chem. A 105, 451

    Article  Google Scholar 

  38. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T., Stenkamp, R.E., Yamamoto, M., Miyano, M. (2000) Science 289, 739

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology Lausanne, 1005, Lausanne, Switzerland

    Ute F. Röhrig, Leonardo Guidoni & Ursula Röthlisberger

  2. Department Chemie, LMU München, Butenandtstr. 5-13, Haus E, 81377, München, Germany

    Stephan Grimm & Irmgard Frank

  3. Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology Zurich, USI-Campus, 6900, Lugano, Switzerland

    Alessandro Laio

Authors
  1. Ute F. Röhrig
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  2. Leonardo Guidoni
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  3. Ursula Röthlisberger
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  4. Stephan Grimm
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  5. Irmgard Frank
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  6. Alessandro Laio
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Editor information

Editors and Affiliations

  1. Institut für Aerodynamik und Gasdynamik, Universität Stuttgart, Pfaffenwaldring 21, 70550, Stuttgart, Germany

    Siegfried Wagner

  2. Institut für Theoretische Physik und Astrophysik, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany

    Werner Hanke

  3. Lehrstuhl für Rechnertechnik und Rechnerorganisation, Institut für Informatik, Technische Universität München, Boltzmannstraße 3, 85748, Garching, Germany

    Arndt Bode

  4. Lehrstuhl für Strömungsmechanik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstraße 4, 91058, Erlangen, Germany

    Franz Durst

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© 2005 Springer-Verlag Berlin Heidelberg

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Röhrig, U.F., Guidoni, L., Röthlisberger, U., Grimm, S., Frank, I., Laio, A. (2005). QM/MM Simulation of the First Step of Vision. In: Wagner, S., Hanke, W., Bode, A., Durst, F. (eds) High Performance Computing in Science and Engineering, Munich 2004. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26657-7_21

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