Leipzig, 17 May 20071 Markov Models of Protein Folding - Application to Molecular Dynamics Simulations Christian Hedegaard Jensen.

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Presentation transcript:

Leipzig, 17 May Markov Models of Protein Folding - Application to Molecular Dynamics Simulations Christian Hedegaard Jensen

Leipzig, 17 May Outline Markov Models and Molecular Dynamics Simulations Investigating Accelerated Molecular Dynamics

Leipzig, 17 May Outline Markov Models and Molecular Dynamics Simulations Investigating Accelerated Molecular Dynamics

Leipzig, 17 May Basic Idea Do many Molecular Dynamics Simulations Cluster the trajectories into discrete states Combine the information about transitions from all the trajectories into a single Markov model transition matrix. This allows for highly parallel simulations. E.g.

Leipzig, 17 May How Sensitive is the Dynamics to Clustering Investigate a small peptide VPAL 500ns MD simulation with explicit water at 300k How sensitive are the mean first passage times between states, to the clustering of the states.

Leipzig, 17 May Calculating Mean First Passage Times

Leipzig, 17 May Cluster Variation

Leipzig, 17 May Sensitivity

Leipzig, 17 May Sensitivity

Leipzig, 17 May Sensitivity

Leipzig, 17 May Outline Markov Models and Molecular Dynamics Simulations Investigating Accelerated Molecular Dynamics

Leipzig, 17 May Accelerated Molecular Dynamics Modify the potential energy landscape to speed up transitions between states. D. Hamelberg, J. Mongan, and J. A. McCammon. Accelerated molecular dynamics: a promising and e±cient simulation method for biomolecules. Journal of Chemical Physics, 120(24): , A. F. Voter. Hyperdynamics: Accelerated molecular dynamics of infrequent events. Physical Review Letters, 78(20): , A. F. Voter. A method for accelerating the molecular dynamics simulation of infrequent events. Journal of Chemical Physics, 106(11): , 1997.

Leipzig, 17 May Scaled Potentials Scale potential by constant Energy differences Assuming transition state theory: similar to changing temperature

Leipzig, 17 May Scaled Potentials Possible use 1: –Do a simulation with  <1 Possible use 2: –Start with  =1 –For every e.g. 10ps in same minima change  = 0.9*  –When in new minima reset  =1 This means that the potentials are modified just enough (and no more) to escape a minima within a reasonable time

Leipzig, 17 May Scaled Potentials Do calculations with different  and investigate the change in mean first passage times between states. Compare to simulations done at different temperatures. If there is a significant speedup implement algorithm.

Leipzig, 17 May Thank you