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Minimize structure [Fix clashes] with OpenMM

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The raw output files for each step of the pipeline can be found here

Documentation

https://github.com/mmagnus/rna-tools/blob/master/rna_tools/tools/md/rna_md.py

P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and V. S. Pande, “OpenMM 7: Rapid development of high performance algorithms for molecular dynamics,” PLoS Comput Biol, vol. 13, no. 7, pp. e1005659–17, Jul. 2017.

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