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. SEMINARI0. 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.



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

  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)