Theoretical Seminars: Difference between revisions

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=== Water models in computer simulation (Ying Xue, 03.09.09) ===
=== Water models in computer simulation (Ying Xue, 03.09.09) ===


1. [[media:Berendsen1981_SPC.pdf‎|Berendsen, HJC, Postma, JPM, van Gunsteren, WF and Hermans, J. (1981) Interaction models
1. [[media:Berendsen1981_SPC.pdf‎|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,
for water in relation to protein hydration. ''In'' Intermolecular Forces; Reidel Ed.; Dordrecht,
The Netherlands, 331–342]]: SPC model.
The Netherlands, 331–342]]: SPC model.

Revision as of 02:08, 2 September 2009

Schedule

See the Group meeting schedule.

Next Theoretical Seminar

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.

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

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)

Clustering methods (Itamar Kass, 30.10.08)