Theoretical Seminars

Schedule

See the Group meeting schedule.

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 | Alpesh
2. Structural Determination | Mitchell
3. How to define Clusters and what can we learn from it on proteins properties? | Itamar
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?

Clustering methods (Itamar Kass, 30.10.08)

• PDF file of the talk here
• Complementary reading:
  1. Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. J. Comput. Chem. 15 (12), 1331-1340
  2. Shao, J et al (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. J. Chem. Theory Comput. 3, 2312-2334
  3. Daura, X et al (1999) Peptide folding: when simulation meets experiment. Angew. Chem. Int. Ed. '38 (1/2), 236-240

Prediction of secondary structures (David Poger, 16.04.09)

More to come soon...