Theoretical Seminars

Schedule

See the Group meeting schedule.

Next Theoretical Seminar

Löwdin Population Analysis (Zhi Guang Jia, 29.07.10)

1. Bruhn, G, Davidson, ER, Mayer, I and Clark, AE (2006) Löwdin population analysis with and without rotational invariance. Int. J. Quantum Chem. 106, 2065–2072.
2. Mayer, I (2004) Löwdin population analysis is not rotationally invariant. Chem. Phys. Lett. 393, 209–212.

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 | David — Done

Past Theoretical Seminars

Molecular surfaces (David Poger, 03.06.10)

• PDF file of the talk here
• Complementary reading:
  1. Lee, B and Richards, FM (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55, 379–400.
  2. Connolly, ML (1983) Analytical molecular surface calculation. J. Appl. Crystallogr. 16, 548–558.

Implicit solvent models (Pramod Nair, 06.05.10)

1. Zhou, R (2003) Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins 53, 148–161.
2. Roux, B and Simonson, T (1999) Implicit solvent models. Biophys. Chem. 78, 1–20.
3. Still, WC, Tempczyk A, Hawley RC and Hendrickson T (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc.' 112, 6127–6129.

Lateral pressure profile calculations for lipid bilayers (Rong Chen, 04.03.10)

1. Lindahl, E and Edholm, O (2000) Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations. J. Chem. Phys. 113, 3882–3893.
2. Sonne, J, Hansen, FY and Peters, GH (2005) Methodological problems in pressure profile calculations for lipid bilayers. J. Chem. Phys. 122, 124903.

Atomic force microscopy (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

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.

‎

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