Lecture
Classical Simulation of (Bio)Molecular Systems (CSBMS)
Prof. Philippe H. Hünenberger + Prof S. Riniker + Dr Jozica Dolenc / HS23
Fall semester 2023 (HS23)
18 September – 22 December 2023
Lecture
Tuesdays, 9.45-11.30 hrs, HCI D2 , ETH Hönggerberg (14x2 hours); lecture No 529-0004-00; note that the break is usually reduced to 5 minutes, so that the actual time is 9.45-11:20 instead
Participants
Chemistry, Chemical Engineering, Interdisciplinary Natural Sciences (IN), Computational Science and Engineering (RW/CSE), Biology, Computational Biology and Bioinformatics (CBB), MAS in Medicinal Physics, ... - usually at the Master level; note that PhD students and postdocs who are interested in learning computer-simulation techniques are also very welcome
Lecturers
Prof. Dr. Philippe H. Hünenberger, , www.csms.ethz.ch
Prof. Dr. Sereina Riniker, , riniker.ethz.ch
Dr. Jozica Dolenc, , infozentrum.ethz.ch/mitarbeiter
Language
The lecture as well as all the written material are in English
Goal
Provide the participants with theoretical and practical knowledge concerning the computer simulation of (bio)molecular systems with a main focus on classical atomistic silumation using molecular dynamics (MD); more precisely, the goals of the course include:
- Understanding the physics, algorithms and approximations underlying these simulations
- Learning how to perform and analyze these simulations in practice (using the GROMOS program)
- Acquiring sufficient experience for the critical interpretation of simulation results and their relationship to experimental data
- Being introduced to a range of applications of simulation techniques in chemistry, physics and biology
| lecture | week | date | lect | theme | exercise |
|---|---|---|---|---|---|
| 1 | 38 | 19.09.2023 | PH | Introduction / Molecular models / GROMOS | - |
| 2 | 39 | 26.09.2023 | PH | Force-fields I | 1 |
| 3 | 40 | 03.10.2023 | PH | Force-fields II | 1 |
| 4 | 41 | 10.10.2023 | PH | Generating configurations | 2 |
| 5 | 42 | 17.10.2023 | PH | Boundary conditions | 2 |
| 6 | 43 | 24.10.2023 | PH | Electrostatic interactions | 3 |
| 7 | 44 | 31.10.2023 | SR | Analysis of simulations | 3 |
| 8 | 45 | 07.11.2023 | SR | Enhanced sampling | 4 |
| 9 | 46 | 14.11.2023 | SR | Free-energy calculations I | 4 |
| 10 | 47 | 21.11.2023 | SR | Free-energy calculations II | 5 |
| 11 | 48 | 28.11.2023 | JD | Structure refinement | 5 |
| 12 | 49 | 05.12.2023 | SR | Multiscale modeling | 6 |
| 13 | 50 | 12.12.2023 | PH+SR | Special topics (Assistant presentations) | 6 |
| 14 | 51 | 19.12.2023 | PH | Answer to thinking questions/ Concluding remarks | - |
Lecture number, calendar week, date, lecturer (PH=Hunenberger,SR=Riniker,JD=Dolenc), theme, and exercise number of the exercise in progress during this week
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 to get their ETH credit points or Zulassungsprüng (but are very welcome to join if they wish)
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