Theoretical Seminars

Schedule

See the Group meeting schedule.

Next Theoretical Seminar

Water models in computer simulation (Roy Le, 03.12.09)

1. Gross L, Mohn F, Moll N, Liljeroth P and Meyer G (2009) The chemical structure of a molecule resolved by atomic force microscopy. Science 325, 1110–1114

Suggested topics

You are more than welcome to suggest topics for future theoretical seminars.

Name of topic | Suggestion by

1. Structural Determination | Mitchell — Done
2. How to define Clusters and what can we learn from it on proteins properties? | Itamar — Done
3. Generating the force field for a heteromolecule | Alpesh — Done
4. Gromacs 4: What's new - What's broken? Breaking the 2fs time step barrier and clever parallelisation.
5. GROMOS2017 – New developments (Coming soon(ish)!)
6. Error in Crystal/NMR Structures and their implications.
7. Determination of secondary structure elements | David — Done
8. SETTLE/RATTLE/timestep: methods for the simulation of water, implications in our simulations in a world that thinks the 2-fs timestep is because of the C–H bond vibration frequency.
9. LINCS/SHAKE/dummy atoms
10. What can be analyzed from simulations? An introduction to the various structural/dynamic properties that can be calculated
11. NMA/PCA/ED: what are these methods? how good are they? what for?
12. Sequence alignment, prediction of secondary structures, homology modelling
13. Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF...
14. Molecular surfaces, NAccess

Past Theoretical Seminars

Water models in computer simulation (Ying Xue, 03.09.09)

1. Berendsen, HJC, Postma, JPM, van Gunsteren, WF and Hermans, J (1981) Interaction models for water in relation to protein hydration. In Intermolecular Forces; Reidel Ed.; Dordrecht, The Netherlands, 331–342: SPC model.
2. Berendsen, HJC, Grigera, JR and Straatsma, TP (1987) The missing term in effective pair potentials. J. Phys. Chem. 91, 6269–6271: SPC/E model.
3. Jorgensen, WL, Chandrasekhar, J, Madura, JD, Impey, RW and Klein, ML (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935: TIP3P model.
4. Mahoney, MW and Jorgensen, WL (2000) A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112, 8910–8922: TIP5P model.
5. Guillot, B (2002) A reappraisal of what we have learnt during three decades of computer simulations on water. J. Mol. Liq. 101, 219–260.

Generating the force field for a heteromolecule (Alpesh Malde, 21.05.09)

1. Oostenbrink, C, Villa, A., Mark, AE and van Gunsteren, WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656–1676: this paper describes the GROMOS 53A5 and 53A6 force field.
2. Lins, RD and Hünenberger, PH (2005) A new GROMOS force field for hexopyranose-based carbohydrates. J. Comput. Chem. 26, 1400–1412: this paper describes generating the force field for sugars.
3. Seminario, JM (1996) Calculation of intramolecular force fields from second-derivative tensors. Int. J. Quantum Chem. S30, 1271-1277: this paper describes how to generate the force constants for bond, angle and dihedral terms from a Hessian matrix of the molecule in the equilibrium geometry using Hess2FF method.

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Determination of secondary structure elements (David Poger, 23.04.09)

• PDF file of the talk here
• Complementary reading:
  1. Kabsch, W and Sander, C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22 (12), 2577-2637: article of reference for DSSP
  2. Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. Proteins 23 (4), 566-579: article of reference for STRIDE
  3. Sklenar, H, Etchebest, C and Lavery, R (1989) Describing protein structure: a general algorithm yielding complete helicoidal parameters and a unique overall axis. Proteins 6 (1), 46-60: algorithm P-Curve
  4. Martin, J, Letellier, G, Marin, A, Taly, J-F, de Brevern, AG, Gibrat JF (2005) Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct. Biol. 5, 17.

Clustering methods (Itamar Kass, 30.10.08)

• PDF file of the talk here
• Complementary reading:
  1. Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 15 (12), 1331-1340
  2. Shao, J et al (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3, 2312-2334
  3. Daura, X et al (1999) Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. '38 (1/2), 236-240