Abstract
The approximation of long time molecular dynamics of proteins by a Markov chain on a discrete set of states (Markov State Model or MSM) allows for a detailed description of equilibrium and kinetic properties of folding. MSMs also allow direct comparison to experimental ensemble observables, which makes them a very appealing tool for analysis of Molecular Dynamics (MD) simulations. Here, we compare MSMs based on three different sets of MD simulations of the Trp-Cage miniprotein with equal sampling of 40 microseconds each. The three sets comprise of several short simulations, some medium lenght simulations and a few long simulations. Statistical and systematic errors on dynamical properties of the resulting models are compared and discussed which will help in the understanding of the construction and analysis of this type of models for more complex systems. We will describe the folding kinetics of the Trp-cage, including structural changes that occur within the folded state. This work has been funded by NSF MCB 1050966
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