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The key enablers have been optimization and parallelization of the simulation codes. However, much of the software used to analyze trajectory data from these simulations is still run in serial, or in some cases many threads via shared memory. Here, we describe the addition of multiple levels of parallel trajectory processing to the molecular dynamics simulation analysis software CPPTRAJ. In addition to the existing OpenMP shared\u2010memory parallelism, CPPTRAJ now has two additional levels of message passing (MPI) parallelism involving both across\u2010trajectory processing and across\u2010ensemble processing. All three levels of parallelism can be simultaneously active, leading to significant speed ups in data analysis of large datasets on the NCSA Blue Waters supercomputer by better leveraging the many available nodes and its parallel file system. \u00a9 2018 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.25382","type":"journal-article","created":{"date-parts":[[2018,10,28]],"date-time":"2018-10-28T10:59:39Z","timestamp":1540724379000},"page":"2110-2117","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":170,"title":["Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data"],"prefix":"10.1002","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5834-2447","authenticated-orcid":false,"given":"Daniel R.","family":"Roe","sequence":"first","affiliation":[{"name":"D. R. Roe Laboratory of Computational Biology National Heart Lung and Blood Institute, National Institutes of Health Bethesda Maryland 20892"}]},{"suffix":"III","given":"Thomas E.","family":"Cheatham","sequence":"additional","affiliation":[{"name":"T. E. Cheatham Department of Medicinal Chemistry College of Pharmacy 2000 South 30 East Room 105, University of Utah, Salt Lake City Utah 84112"}]}],"member":"311","published-online":{"date-parts":[[2018,10,3]]},"reference":[{"key":"e_1_2_5_1_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct200909j"},{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1021\/ct400314y"},{"key":"e_1_2_5_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21209"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20829"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1145\/1364782.1364802"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0009-2614(99)01123-9"},{"key":"e_1_2_5_7_1","author":"Bergonzo C.","year":"2013","journal-title":"J. Chem. 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