Theoretical Seminars: Difference between revisions

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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).
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.
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 ==
== Suggested topics ==

Revision as of 01:47, 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.

Suggested topics

You are more than welcome to suggest topics for future theoretical seminars.

Name of topic | Suggestion by

  1. Soft Core non-bonded interactions
  2. Structural Determination | Mitchell — Done
  3. How to define Clusters and what can we learn from it on proteins properties? | Itamar — 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 Structures and its implications. Can MD be used for X-ray structure refinement?
  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

Determination of secondary structure elements (David Poger, 23.04.09)

Clustering methods (Itamar Kass, 30.10.08)