Theoretical Seminars: Difference between revisions
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== Next Theoretical Seminar: | == Next Theoretical Seminar: | ||
== Suggested topics == | == Suggested topics == | ||
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== Past Theoretical Seminars == | == Past Theoretical Seminars == | ||
===''Generating the force field for a heteromolecule'' (Alpesh Malde, 21.05.09) === | |||
1. [[media:Gromos53a5a6.pdf|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. [[media:Gromos_sugar_Hünenberger.pdf|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. [[media:Seminario_Hess2FF.pdf|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) === | === Determination of secondary structure elements (David Poger, 23.04.09) === | ||
* PDF file of the talk [[Media:Secondary_structures.pdf|here]] | * PDF file of the talk [[Media:Secondary_structures.pdf|here]] |
Revision as of 22:13, 27 May 2009
Schedule
See the Group meeting schedule.
== Next Theoretical Seminar:
Suggested topics
You are more than welcome to suggest topics for future theoretical seminars.
Name of topic | Suggestion by
- Structural Determination | Mitchell — Done
- How to define Clusters and what can we learn from it on proteins properties? | Itamar — Done
- Generating the force field for a heteromolecule | Alpesh — Done
- Gromacs 4: What's new - What's broken? Breaking the 2fs time step barrier and clever parallelisation.
- GROMOS2017 – New developments (Coming soon(ish)!)
- Error in Crystal/NMR Structures and their implications.
- Determination of secondary structure elements | David — Done
- 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.
- LINCS/SHAKE/dummy atoms
- What can be analyzed from simulations? An introduction to the various structural/dynamic properties that can be calculated
- NMA/PCA/ED: what are these methods? how good are they? what for?
- Sequence alignment, prediction of secondary structures, homology modelling
- Of the history of MD: differences between all these forcefields that we always talk about: GROMOS, CHARMM, OPLS, AMBER, GROMACS, GAFF...
- Molecular surfaces, NAccess
Past Theoretical Seminars
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:
- 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
- Frishman, D and Argos, P (1995) Knowledge-based protein secondary structure assignment. Proteins 23 (4), 566-579: article of reference for STRIDE
- 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
- 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:
- Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 15 (12), 1331-1340
- Shao, J et al (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3, 2312-2334
- Daura, X et al (1999) Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. '38 (1/2), 236-240