Theoretical Seminars

From MDWiki
Jump to navigationJump to search

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

  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)