Lecture

Course material

• The lecture slides in pdf format will be available on this site latest on the evening before the lecture (see the documents page)
• If there are significant changes between this pdf and the slides of the lecture as given, an updated pdf may also be posted after the lecture (within a day)

Requirements

• To take advantage of the lectures, a good general knowledge of mathematics, physics, chemistry and biology is required
• To take advantage of the exercises, a basic knowledge of computer science and a good practical knowledge of the UNIX operating system are required
  

Assessment

• The assessment of the course consists of an oral examination of 30 minutes duration, probing the entire content of the lecture
• Since the practical exercises do convey different skills as those being conveyed during the lectures, the performance in the exercises are taken into account in the final exam mark (learning component, possible bonus of up to 0.25 points on the exam mark)
• Bachelor and Master students must do the practical exercises (and take the exam)
• Ph.D. students and postdocs need not do the practical exercises (still, they are very welcome to join if they wish), but PhD students must take the exam to get their ETH credit points or in case of Zulassungsprüng
  

Literature

• 90.6 W.F. van Gunsteren and H.J.C. Berendsen Computer Simulation of Molecular Dynamics: Methodology, Applications and Perspectives in Chemistry Angew. Chem. Int. Ed. Engl. 29 (1990) 992-1023
• 93.28 W.F. van Gunsteren Molecular dynamics and stochastic dynamics simulation: A primer In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 3-36
• 99.11 W.R.P. Scott, P.H. Hünenberger, I.G. Tironi, A.E. Mark, S.R. Billeter, J. Fennen, A.E. Torda, T. Huber, P. Krüger and W.F. van Gunsteren The GROMOS Biomolecular Simulation Program Package J. Phys. Chem. A 103 (1999) 3596-3607
• 05.32 M. Christen, P.H. Hünenberger, D. Bakowies, R. Baron, R. Bürgi, D.P. Geerke, T.N. Heinz, M.A. Kastenholz, V. Kräutler, C. Oostenbrink, C. Peter, D. Trzesniak, W.F. van Gunsteren The GROMOS software for biomolecular simulation: GROMOS05 J. Comput. Chem. 26 (2005) 1719-1751
• 06.16 W.F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D.P. Geerke, A. Glättli, P.H. Hünenberger, M.A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N.F.A. van der Vegt and H.B. Yu Biomolecular modelling: goals, problems, perspectives Angew. Chem 118 (2006) 4168-4198, Angew. Chem. Int. Ed. 45 (2006) 4064-4092
• 97.25 P.H. Hünenberger and W.F. van Gunsteren Empirical classical interaction functions for molecular simulation In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 3, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, (1997), pp. 3-82
• 93.31 P.E. Smith and W.F. van Gunsteren Methods for the evaluation of long-range electrostatic forces in computer simulations of molecular systems In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 182-212
• 93.29 W.F. van Gunsteren, T.C. Beutler, F. Fraternali, P.M. King, A.E. Mark and P.E. Smith Computation of free energy in practice: choice of approximations and accuracy limiting factors In: "Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications", Vol. 2, W.F. van Gunsteren, P.K. Weiner, A.J. Wilkinson eds., Escom Science Publishers, Leiden, The Netherlands, (1993), pp. 315-348
• 07.19 M. Christen, W.F. van Gunsteren On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review J. Comput. Chem. 29 (2007) 157-166 (DOI: 10.1002/jcc.20725)
• 94.26 W.F. van Gunsteren, R.M. Brunne, P. Gros, R.C. van Schaik, C.A. Schiffer and A.E. Torda Accounting for Molecular Mobility in Structure Determination Based on Nuclear, Magnetic Resonance Spectroscopic and X-Ray Diffraction Data. In: "Methods in Enzymology: Nuclear Magnetic Resonance", Vol. 239, T.L. James,N.J. Oppenheimer eds., Academic Press, New York, (1994), pp. 619-654
• 99.14 W.F. van Gunsteren, A.M.J.J. Bonvin, X. Daura and L.J. Smith Aspects of Modeling Biomolecular Structure on the Basis of Spectroscopic or Diffraction Data In "Structure Computation and Dynamics in Protein NMR", Biol. Magnetic Resonance Vol. 17, Krishna and Berliner eds., Plenum Publishers, New York, 1999, pp.3-35
• 98.3 W.F. van Gunsteren and A.E. Mark Validation of molecular dynamics simulation J. Chem. Phys. 108 (1998) 6109-6116
• 16.08 W. F. van Gunsteren, J. R. Allison, X. Daura, J. Dolenc, N. Hansen, A. E. Mark, C. Oostenbrink, V. H. Rusu, L. J. Smith Deriving structural information from experimentally measured data on biomolecules: a review, Angew. Chem. Int. Ed. 55 (2016) 15990-16010