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With femtosecond integration steps, microsecond simulations generate billions of time steps with a complete set of atomic positions, velocities, and forces for all atoms, corresponding to petabytes of data and exceeding typical storage capacities. Consequently, only a fraction of the simulated time steps are usually written to a trajectory file for subsequent analysis, often at time intervals of 10\u2013100 ps. Such a trajectory file allows for the analysis of ensemble averages and slow dynamics, but information on faster processes is lost. These fast processes include intra- and intermolecular vibrations, dynamics in nonglassy solvents, short-lived transition states, transport properties, etc., which encode physical information and are related to fundamental macroscopic properties and experimental observables. Here, we introduce a data streaming interface for MD simulations that provides easy access to all data generated during a running simulation. Instead of writing data to a storage medium, our interface enables user-defined analysis routines that access live simulation data via streaming. For this purpose, we build on existing implementations of the Interactive Molecular Dynamics (IMD) protocol and implement an enhanced protocol (termed IMD version 3 or \u2018IMDv3\u2032) in three popular MD packages: GROMACS, NAMD, and LAMMPS. Our new Python package imdclient receives an IMDv3 data stream and makes it available for other applications. To maximize usability, we added the capability to process streamed MD simulation data to the popular MDAnalysis software package. We demonstrate increased simulation performance for streaming compared to simulations that write data at high frequency to a trajectory output file. We include usage examples that illustrate live monitoring of custom variables during a running simulation, evaluation of velocity time correlation functions with fast fluctuations, and instantaneous analysis of currents through a membrane pore.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c01055","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T18:36:22Z","timestamp":1788460582000},"page":"9260-9273","source":"Crossref","is-referenced-by-count":0,"title":["Streaming Molecular\nDynamics Simulation Data for On-the-Fly\nProcessing and Analysis"],"prefix":"10.1021","volume":"22","author":[{"given":"Amruthesh","family":"Thirumalaiswamy","sequence":"first","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawson J.","family":"Woods","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]},{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heekun","family":"Cho","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7393-7457","authenticated-orcid":true,"given":"Hugo","family":"MacDermott-Opeskin","sequence":"additional","affiliation":[{"name":"NumFOCUS , , , ,","place":["Austin, Texas, United States, 78730"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4897-5651","authenticated-orcid":true,"given":"Jennifer","family":"Clark","sequence":"additional","affiliation":[{"name":"NumFOCUS , , , ,","place":["Austin, Texas, United States, 78730"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irfan","family":"Alibay","sequence":"additional","affiliation":[{"name":"NumFOCUS , , , ,","place":["Austin, Texas, United States, 78730"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxuan","family":"Zhuang","sequence":"additional","affiliation":[{"name":"NumFOCUS , , , ,","place":["Austin, Texas, United States, 78730"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1340-0831","authenticated-orcid":true,"given":"Oliver","family":"Beckstein","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]},{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7956-5287","authenticated-orcid":true,"given":"Matthias","family":"Heyden","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]},{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"2026092209072502600_cit1","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-59745-177-2_1","volume-title":"Molecular Modeling\nof Proteins","author":"Lindahl","year":"2008"},{"key":"2026092209072502600_cit2","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","article-title":"Molecular Dynamics Simulation for\nAll","volume":"99","author":"Hollingsworth","year":"2018","journal-title":"Neuron"},{"key":"2026092209072502600_cit3","volume-title":"Understanding Molecular Simulation:\nFrom Algorithms to Applications","author":"Frenkel","year":"2023"},{"key":"2026092209072502600_cit4","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1021\/ar010033z","article-title":"Molecular\ndynamics simulations of biological reactions","volume":"35","author":"Warshel","year":"2002","journal-title":"Acc. Chem. Res."},{"key":"2026092209072502600_cit5","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1021\/cr040426m","article-title":"Molecular dynamics: survey of methods for simulating\nthe activity of proteins","volume":"106","author":"Adcock","year":"2006","journal-title":"Chem. Rev."},{"key":"2026092209072502600_cit6","doi-asserted-by":"publisher","DOI":"10.1002\/wcms.1393","article-title":"Biomolecular\nsimulations: From dynamics\nand mechanisms to computational assays of biological activity","volume":"9","author":"Huggins","year":"2019","journal-title":"WIREs Comput. Mol. Sci."},{"key":"2026092209072502600_cit7","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1021\/accountsmr.1c00238","article-title":"Learning matter:\nMaterials design\nwith machine learning and atomistic simulations","volume":"3","author":"Axelrod","year":"2022","journal-title":"Acc. Mater. Res."},{"key":"2026092209072502600_cit8","doi-asserted-by":"publisher","first-page":"3059","DOI":"10.1021\/ie901898k","article-title":"Historical perspective and current\noutlook for molecular\ndynamics as a chemical engineering tool","volume":"49","author":"Maginn","year":"2010","journal-title":"Ind.\nEng. Chem. Res."},{"key":"2026092209072502600_cit9","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1021\/acs.accounts.2c00811","article-title":"Non-equilibrium\nmodeling of concentration-driven processes with constant chemical\npotential molecular dynamics simulations","volume":"56","author":"Karmakar","year":"2023","journal-title":"Acc.\nChem. Res."},{"key":"2026092209072502600_cit10","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1038\/nature06522","article-title":"Dynamic personalities of proteins","volume":"450","author":"Henzler-Wildman","year":"2007","journal-title":"Nature"},{"key":"2026092209072502600_cit11","doi-asserted-by":"publisher","first-page":"558","DOI":"10.1002\/jcc.23973","article-title":"Accurately\nmodeling nanosecond protein dynamics requires at least microseconds\nof simulation","volume":"37","author":"Bowman","year":"2016","journal-title":"J. Comput. Chem."},{"key":"2026092209072502600_cit12","doi-asserted-by":"crossref","unstructured":"Shaw, D. E.; Adams, P. J.; Azaria, A.; Bank, J. A.; Batson, B.; Bell, A.; Bergdorf, M.; Bhatt, J.; Butts, J. A.; Correia, T.; Dirks, R. M.; Dror, R. O.; Eastwood, M. P.; Edwards, B.; Even, A.; Feldmann, P.; Fenn, M.; Fenton, C. H.; Forte, A.; Gagliardo, J.; Gill, G.; Gorlatova, M.; Greskamp, B.; Grossman, J. 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In  Anton 3: Twenty Microseconds of Molecular\nDynamics Simulation before Lunch, Proceedings of the International\nConference for High Performance Computing, Networking, Storage and\nAnalysis; ACM, 2021;\npp 1\u201311.","DOI":"10.1145\/3458817.3487397"},{"key":"2026092209072502600_cit13","doi-asserted-by":"publisher","DOI":"10.1063\/1.5081739","article-title":"Heterogeneity\nof water structure and dynamics at the protein-water interface","volume":"150","author":"Heyden","year":"2019","journal-title":"J. Chem. Phys."},{"key":"2026092209072502600_cit14","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-3-319-64203-1_1","article-title":"Computing\nJust What You Need: Online Data Analysis and Reduction at Extreme\nScales. 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Sci. U.S.A."},{"key":"2026092209072502600_cit18","doi-asserted-by":"publisher","first-page":"5481","DOI":"10.1021\/acs.jctc.2c01309","article-title":"Frequency-Selective Anharmonic Mode Analysis of Thermally\nExcited Vibrations in Proteins","volume":"19","author":"Sauer","year":"2023","journal-title":"J. Chem. Theory\nComput."},{"key":"2026092209072502600_cit19","doi-asserted-by":"publisher","first-page":"4467","DOI":"10.1021\/acs.jctc.7b00184","article-title":"Signatures\nof solvation thermodynamics in spectra of intermolecular vibrations","volume":"13","author":"Persson","year":"2017","journal-title":"J. Chem. Theory Comput."},{"key":"2026092209072502600_cit20","doi-asserted-by":"publisher","first-page":"7063","DOI":"10.1073\/pnas.1136844100","article-title":"Liquid-vapor oscillations of water\nin hydrophobic nanopores","volume":"100","author":"Beckstein","year":"2003","journal-title":"Proc. Natl. Acad.\nSci. 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Rev. Phys. Chem."},{"key":"2026092209072502600_cit24","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1126\/science.1183723","article-title":"Efficient\nAnnealing of Radiation Damage Near Grain Boundaries via Interstitial\nEmission","volume":"327","author":"Bai","year":"2010","journal-title":"Science"},{"key":"2026092209072502600_cit25","doi-asserted-by":"publisher","DOI":"10.1063\/1.2713401","article-title":"New method\nto analyze simulations\nof activated processes","volume":"126","author":"Wedekind","year":"2007","journal-title":"J. Chem. Phys."},{"key":"2026092209072502600_cit26","doi-asserted-by":"publisher","first-page":"5833","DOI":"10.1073\/pnas.0911691107","article-title":"Principles\nof conduction and hydrophobic gating in K+ channels","volume":"107","author":"Jensen","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026092209072502600_cit27","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1126\/science.1187409","article-title":"Atomic-Level Characterization of\nthe Structural Dynamics of Proteins","volume":"330","author":"Shaw","year":"2010","journal-title":"Science"},{"key":"2026092209072502600_cit28","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nchembio.202","article-title":"Enzymatic transition\nstates and dynamic motion in barrier\ncrossing","volume":"5","author":"Schwartz","year":"2009","journal-title":"Nat. Chem. Biol."},{"key":"2026092209072502600_cit29","doi-asserted-by":"crossref","unstructured":"Bennett, J. C.; Abbasi, H.; Bremer, P.-T.; Grout, R.; Gyulassy, A.; Jin, T.; Klasky, S.; Kolla, H.; Parashar, M.; Pascucci, V.; Pebay, P.; Thompson, D.; Yu, H.; Zhang, F.; Chen, J. In  Combining\nIn-Situ and in-Transit Processing to Enable Extreme-Scale Scientific\nAnalysis, Proceedings of the International Conference on\nHigh Performance Computing, Networking, Storage and Analysis; IEEE: Washington, DC, USA, 2012.","DOI":"10.1109\/SC.2012.31"},{"key":"2026092209072502600_cit30","doi-asserted-by":"crossref","unstructured":"Lakshminarasimhan, S.; Boyuka, D. A.; Pendse, S. V.; Zou, X.; Jenkins, J.; Vishwanath, V.; Papka, M. E.; Samatova, N. F. In  Scalable In Situ\nScientific Data Encoding for Analytical Query Processing,\nProceedings of the 22nd International Symposium on High-performance\nParallel and Distributed Computing; IEEE: New York, NY, USA, 2013; pp 1\u201312.","DOI":"10.1145\/2493123.2465527"},{"key":"2026092209072502600_cit31","doi-asserted-by":"crossref","unstructured":"Stone, J. E.; Gullingsrud, J.; Schulten, K. In  A System for Interactive\nMolecular Dynamics Simulation, Proceedings of the 2001 Symposium\non Interactive 3D Graphics; ACM: New York, NY, USA, 2001; pp 191\u2013194.","DOI":"10.1145\/364338.364398"},{"key":"2026092209072502600_cit32","doi-asserted-by":"publisher","first-page":"W483","DOI":"10.1093\/nar\/gkac398","article-title":"MDsrv:\nvisual sharing and analysis of molecular dynamics simulations","volume":"50","author":"Kampfrath","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2026092209072502600_cit33","doi-asserted-by":"crossref","unstructured":"Dreher, M.; Raffin, B. In  A Flexible Framework\nfor Asynchronous in Situ and in Transit Analytics for Scientific Simulations, 2014 14th IEEE\/ACM International Symposium on Cluster, Cloud and\nGrid Computing; IEEE: Chicago, IL, USA, 2014; pp 277\u2013286.","DOI":"10.1109\/CCGrid.2014.92"},{"key":"2026092209072502600_cit34","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1002\/jcc.24729","article-title":"In situ data\nanalytics and indexing of protein trajectories","volume":"38","author":"Johnston","year":"2017","journal-title":"J. Comput. Chem."},{"key":"2026092209072502600_cit35","doi-asserted-by":"crossref","unstructured":"Malakar, P.; Knight, C.; Munson, T.; Vishwanath, V.; Papka, M. E. In  Scalable In situ Analysis\nof Molecular Dynamics Simulations, ISAV\u201917 Proceedings\nof the In Situ Infrastructures on Enabling Extreme-Scale Analysis\nand Visualization; ACM: Denver, CO, USA, 2017; pp 1\u20136.","DOI":"10.1145\/3144769.3144772"},{"key":"2026092209072502600_cit36","doi-asserted-by":"crossref","unstructured":"Wolf, M.; Raffin, B.; Mures, O. A.; Padro\u0301n, E. J. In  In-transit Molecular\nDynamics Analysis with Apache Flink, Proceedings of the Workshop\non In Situ Infrastructures for Enabling Extreme-Scale Analysis and\nVisualization; ACM, 2018; pp 25\u201332.","DOI":"10.1145\/3281464.3281469"},{"key":"2026092209072502600_cit37","unstructured":"Grayson, P.; Gullingsrud, J.; Schulten, K.; Stone, J. 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In  MDAnalysis: A Python\nPackage for the Rapid Analysis of Molecular Dynamics Simulations, Proceedings of the 15th Python in Science Conference; SciPy: Austin, TX, 2016; pp 102\u2013109.","DOI":"10.25080\/Majora-629e541a-00e"},{"key":"2026092209072502600_cit44","unstructured":"Woods, L. J.; Beckstein, O.; Thirumalaiswamy, A.; Heyden, M.\n          IMDv3 Protocol\n          2025\n          https:\/\/imdclient.readthedocs.io\/en\/latest\/protocol_v3.html. (Accessed: July 24, 2026)."},{"key":"2026092209072502600_cit45","unstructured":"Woods, L.; Thirumalaiswamy, A.; Cho, H.; MacDermott-Opeskin, H.; Clark, J. A.; Heyden, M.; Beckstein, O.\n          imdclient\n          2025\n          10.5281\/zenodo.20275368."},{"key":"2026092209072502600_cit46","unstructured":"Gowers, R.; Beckstein, O.; Linke, M.; Alibay, I.; Barnoud, J.; Reddy, T.; MacDermott-Opeskin, H.; Meli, R.; Wang, L.; Bansal, U.; Zeman, J.; Detlefs, J.; Dotson, D. L.; Melo, M. 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In  LAMMPS-KOKKOS: Performance Portable Molecular\nDynamics Across Exascale Architectures, Proceedings of the\nSC \u201925 Workshops of the International Conference for High Performance\nComputing, Networking, Storage and Analysis; ACM: New York, NY, USA, 2025; pp 1217\u20131232.","DOI":"10.1145\/3731599.3767498"},{"key":"2026092209072502600_cit49","unstructured":"Woods, L.; Thirumalaiswamy, A.; Beckstein, O.; Heyden, M.\n          modified version\nof LAMMPS with support for data streaming via IMDv3. 202610.5281\/zenodo.20128193."},{"key":"2026092209072502600_cit50","doi-asserted-by":"publisher","DOI":"10.1063\/5.0014475","article-title":"Scalable molecular\ndynamics on CPU and GPU Architectures with NAMD","volume":"153","author":"Phillips","year":"2020","journal-title":"J. Chem. Phys."},{"key":"2026092209072502600_cit51","doi-asserted-by":"publisher","DOI":"10.21105\/joss.07943","article-title":"Zarrtraj:\nA Python package for streaming molecular\ndynamics trajectories from cloud services","volume":"11","author":"Woods","year":"2026","journal-title":"J.\nOpen Source Software"},{"key":"2026092209072502600_cit52","doi-asserted-by":"crossref","unstructured":"Jennewein, D. M.; Lee, J.; Kurtz, C.; Dizon, W.; Shaeffer, I.; Chapman, A.; Chiquete, A.; Burks, J.; Carlson, A.; Mason, N.; Kobawala, A.; Jagadeesan, T.; Basani, P. B.; Battelle, T.; Belshe, R.; McCaffrey, D.; Brazil, M.; Inumella, C.; Kuznia, K.; Buzinski, J.; Shah, D. D.; Dudley, S. M.; Speyer, G.; Yalim, J. 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