MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories . McGibbon, R.; Beauchamp, K.; Harrigan, M.; Klein, C.; Swails, J.; Hernández, C.; Schwantes, C.; Wang, L.; Lane, T.; and Pande, V. Biophysical Journal , 109(8):1528 - 1532, 2015.
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories  [link]Paper  doi  abstract   bibtex   
Abstract As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing \MD\ simulations. \MDTraj\ reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between \MD\ data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. \MDTraj\ is a powerful and user-friendly software package that simplifies the analysis of \MD\ data and connects these datasets with the modern interactive data science software ecosystem in Python.
@article{McGibbon2015mdtraj,
  abstract = {Abstract As molecular dynamics (MD) simulations continue to evolve into powerful computational tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use software tools for the analysis of these simulations is growing. We have developed MDTraj, a modern, lightweight, and fast software package for analyzing \{MD\} simulations. \{MDTraj\} reads and writes trajectory data in a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including minimal root-mean-square-deviation calculations, secondary structure assignment, and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between \{MD\} data and the rapidly growing collection of industry-standard statistical analysis and visualization tools in Python. \{MDTraj\} is a powerful and user-friendly software package that simplifies the analysis of \{MD\} data and connects these datasets with the modern interactive data science software ecosystem in Python. },
  author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X. and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
  doi = {http://dx.doi.org/10.1016/j.bpj.2015.08.015},
  interhash = {840a93815291bff94ed54d2c504c5315},
  intrahash = {2135c61993c8890166eca99310d4300b},
  issn = {0006-3495},
  journal = {Biophysical Journal },
  number = 8,
  pages = {1528 - 1532},
  title = {MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories },
  url = {http://www.sciencedirect.com/science/article/pii/S0006349515008267},
  volume = 109,
  year = 2015
}
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