Theoretical Seminars

Schedule

See the Group meeting schedule.

Next Theoretical Seminar: Generating the force field for a heteromolecule (Alpesh Malde, 21.05.09)

• Papers that would be good to read:

1. CHRIS OOSTENBRINK, ALESSANDRA VILLA, ALAN E. MARK, WILFRED F. VAN GUNSTEREN. 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, 2004. This paper describes the GROMOS 53A5 and 53A6 force field.

2. ROBERTO D. LINS, PHILIPPE H. HUNENBERGER. A New GROMOS Force Field for Hexopyranose-Based Carbohydrates. J Comput Chem 26: 1400–1412, 2005. This paper describes generating the force field for sugars.

3. JORGE M. SEMINARIO. Calculation of Intramolecular Force Fields from Second-Derivative Tensors. International Journal of Quantum Chemistry: Quantum Chemistry Symposium 30, 1271 -1277 (1996). 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. ‎

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

Past Theoretical Seminars

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