References¶
- Michaud-Agrawal2011
N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. J Comp Chem, 32:2319-2327, 2011. doi:10.1002/jcc.21787.
- Gowers2016
R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domański, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102 – 109, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e.
- Khoshlessan2017
M. Khoshlessan, I. Paraskevakos, S. Jha, and O. Beckstein. Parallel analysis in MDAnalysis using the Dask parallel computing library. In Katy Huff, David Lippa, Dillon Niederhut, and M. Pacer, editors, Proceedings of the 16th Python in Science Conference, pages 64–72, Austin, TX, 2017. SciPy. doi:10.25080/shinma-7f4c6e7-00a.
- Paraskevakos2018
Ioannis Paraskevakos, Andre Luckow, Mahzad Khoshlessan, George Chantzialexiou, Thomas E. Cheatham, Oliver Beckstein, Geoffrey C. Fox and Shantenu Jha. Task- parallel Analysis of Molecular Dynamics Trajectories. In 47th International Conference on Parallel Processing (ICPP 2018). doi: 10.1145/3225058.3225128.
- Fan2019
Shujie Fan, Max Linke, Ioannis Paraskevakos, Richard J. Gowers, Michael Gecht, and Oliver Beckstein. PMDA - Parallel Molecular Dynamics Analysis. In Chris Calloway, David Lippa, Dillon Niederhut, and David Shupe, editors, Proceedings of the 18th Python in Science Conference,pages 134 – 142, Austin, TX, 2019. doi:10.25080/Majora-7ddc1dd1-013.
- Awtrey2019
Awtrey, Nikolaus. SPIDAL Summer REU 2019: Parallelizing DensityAnalysis and RMSF in PMDA. Technical report, Arizona State University, Tempe, AZ, 2019. doi: 10.6084/m9.figshare.9695852.