Vienna, Simulating Protein Folding - Some Ideas Christian Hedegaard Jensen Dmitry Nerukh

Vienna, Outline Introduction Transition Matrix Wang-Landau

Vienna, Outline Introduction Transition Matrix Wang-Landau

Vienna, 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)

Vienna, Outline Introduction Transition Matrix Wang-Landau

Vienna, 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.

Vienna, Transition Matrix

Vienna, Transition Matrix

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

Vienna, Transition Matrix Ramachandran Plot

Vienna, Transition Matrix

Vienna, Transition Matrix

Vienna, 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.

Vienna, Outline Introduction Transition Matrix Wang-Landau

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

Vienna, 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).

Vienna, Wang-Landau 0 22 dos 

Vienna, 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.

Vienna, Wang-Landau Matlab

Vienna, Thank you!