Theoretical Seminars: Difference between revisions
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This paper describes generating the force field for sugars. | This paper describes generating the force field for sugars. | ||
3. JORGE M. | 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. | 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. | ||
Revision as of 01:46, 5 May 2009
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.
4. A chapter from the thesis of Marcel Swart on the parameterization of the force-field from quantum chemical calculation data. The work described IntraFF method to generate the force constants from Hessian.
Suggested topics
You are more than welcome to suggest topics for future theoretical seminars.
Name of topic | Suggestion by
- Soft Core non-bonded interactions
- Structural Determination | Mitchell — Done
- How to define Clusters and what can we learn from it on proteins properties? | Itamar — 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 Structures and its implications. Can MD be used for X-ray structure refinement?
- 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
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