1. Vienna, 22-05-20061 Simulating Protein Folding - Some Ideas Christian Hedegaard Jensen Dmitry Nerukh

2. Vienna, 22-05-20062 Outline Introduction Transition Matrix Wang-Landau

3. Vienna, 22-05-20063 Outline Introduction Transition Matrix Wang-Landau

4. Vienna, 22-05-20064 Introduction We are simulation protein folding using Molecular Dynamics, and understanding using complexity analysis. Try to do statistics on trajectories, to see if there are any patterns in where they go. (Transition Matrix) Try and look at the paths that a protein can take when it folds. (Wang-Landau)

5. Vienna, 22-05-20065 Outline Introduction Transition Matrix Wang-Landau

6. Vienna, 22-05-20066 Transition Matrix Find states in trajectory Find transitions between states in trajectory Write up transition matrix for system Possibly include some memory into the system.

7. Vienna, 22-05-20067 Transition Matrix

8. Vienna, 22-05-20068 Transition Matrix

9. Vienna, 22-05-20069 Transition Matrix We have a molecular dynamics simulation of a tripeptide. Trianaline 300 K, 1 atm 12 ps (2fs) OPLSAA-2001 force field GROMACS

10. Vienna, 22-05-200610 Transition Matrix Ramachandran Plot

11. Vienna, 22-05-200611 Transition Matrix

12. Vienna, 22-05-200612 Transition Matrix

13. Vienna, 22-05-200613 Transition Matrix Gives useful information about what is going on in the system. Find out where we end and with what probabilities. Look at transitions between clusters of states.

14. Vienna, 22-05-200614 Outline Introduction Transition Matrix Wang-Landau

15. Vienna, 22-05-200615 Wang-Landau Wang-Landau simulations, using a combination of Molecular Dynamics and Monte Carlo.

16. Vienna, 22-05-200616 Wang-Landau Wang-Landau gives the (relative) density of states. The dos of a simple protein was obtained, d(E). Try to calculate d( ,E) or d( ,,E).

17. Vienna, 22-05-200617 Wang-Landau 0 22 dos 

18. Vienna, 22-05-200618 Wang-Landau Define reaction coordinates Sample as function of these coordinates Method does not say what the system does, but is says what is possible.

19. Vienna, 22-05-200619 Wang-Landau Matlab

20. Vienna, 22-05-200620 Thank you!