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Chodera JD*, Singhal N*, Swope WC, Pande VS, and Dill KA. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics J. Chem. Phys. 126(15):155101 (2007). * These authors contributed equally to the work. (2007)    View

Provide datasets of a model system for the study of biomolecular thermodynamics and kinetics.


This project is a collection of datasets of the alanine dipeptide (more specifically, terminally-blocked alanine peptide) in explicit solvent. These datasets cover both thermodynamic simulations (parallel tempering) and kinetic simulations (Hamiltonian dynamics trajectories) useful for testing algorithms analyzing the thermodynamics and kinetics of biomolecular systems. This model system has already been used in several research papers.

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Alanine dipeptide trajectory data generated with AMBER useful for testing various simulation algorithms

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