Simulating Protein Folding Some Ideas Christian Hedegaard Jensen
- Slides: 20
Simulating Protein Folding - Some Ideas Christian Hedegaard Jensen Dmitry Nerukh Vienna, 22 -05 -2006 1
Outline • Introduction • Transition Matrix • Wang-Landau Vienna, 22 -05 -2006 2
Outline • Introduction • Transition Matrix • Wang-Landau Vienna, 22 -05 -2006 3
Introduction • We are simulation protein folding using Molecular Dynamics, and understanding using complexity analysis. • Try to do statistics on trajectories, to see if there 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, 22 -05 -2006 4
Outline • Introduction • Transition Matrix • Wang-Landau Vienna, 22 -05 -2006 5
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, 22 -05 -2006 6
Transition Matrix Vienna, 22 -05 -2006 7
Transition Matrix Vienna, 22 -05 -2006 8
Transition Matrix • We have a molecular dynamics simulation of a tripeptide. • Trianaline • 300 K, 1 atm • 12 ps (2 fs) • OPLSAA-2001 force field • GROMACS Vienna, 22 -05 -2006 9
Transition Matrix Ramachandran Plot Vienna, 22 -05 -2006 10
Transition Matrix Vienna, 22 -05 -2006 11
Transition Matrix Vienna, 22 -05 -2006 12
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, 22 -05 -2006 13
Outline • Introduction • Transition Matrix • Wang-Landau Vienna, 22 -05 -2006 14
Wang-Landau • Wang-Landau simulations, using a combination of Molecular Dynamics and Monte Carlo. Vienna, 22 -05 -2006 15
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, 22 -05 -2006 16
Wang-Landau dos 0 Vienna, 22 -05 -2006 2 p 17
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, 22 -05 -2006 18
Wang-Landau • Matlab Vienna, 22 -05 -2006 19
Thank you! Vienna, 22 -05 -2006 20
