NAMD goes quantum: an integrative suite for hybrid simulations von Melo, Marcelo C R, Bernardi, Rafael C, Rudack, Till, Scheurer, Maximilian, Riplinger, Christoph, Phillips, James C, Maia, Julio D C, Rocha, Gerd B, Ribeiro, João V, Stone, John E, Neese, Frank, Schulten, Klaus, Luthey-Schulten, Zaida

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Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps von Singharoy, Abhishek, Teo, Ivan, McGreevy, Ryan, Stone, John E, Zhao, Jianhua, Schulten, Klaus

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QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts von Ribeiro, João V., Bernardi, Rafael C., Rudack, Till, Stone, John E., Phillips, James C., Freddolino, Peter L., Schulten, Klaus

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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics von Casalino, Lorenzo, Dommer, Abigail C, Gaieb, Zied, Barros, Emilia P, Sztain, Terra, Ahn, Surl-Hee, Trifan, Anda, Brace, Alexander, Bogetti, Anthony T, Clyde, Austin, Ma, Heng, Lee, Hyungro, Turilli, Matteo, Khalid, Syma, Chong, Lillian T, Simmerling, Carlos, Hardy, David J, Maia, Julio DC, Phillips, James C, Kurth, Thorsten, Stern, Abraham C, Huang, Lei, McCalpin, John D, Tatineni, Mahidhar, Gibbs, Tom, Stone, John E, Jha, Shantenu, Ramanathan, Arvind, Amaro, Rommie E

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Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation von Roberts, Elijah, Stone, John E., Luthey-Schulten, Zaida

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TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD von Vermaas, Josh V, Hardy, David J, Stone, John E, Tajkhorshid, Emad, Kohlmeyer, Axel

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GPU-accelerated molecular modeling coming of age von Stone, John E., Hardy, David J., Ufimtsev, Ivan S., Schulten, Klaus

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Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating von Gamini, Ramya, Han, Wei, Stone, John E, Schulten, Klaus

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OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems von Stone, John E., Gohara, David, Shi, Guochun

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GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting von Stone, John E, McGreevy, Ryan, Isralewitz, Barry, Schulten, Klaus

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Stable Small Quantum Dots for Synaptic Receptor Tracking on Live Neurons von Cai, En, Ge, Pinghua, Lee, Sang Hak, Jeyifous, Okunola, Wang, Yong, Liu, Yanxin, Wilson, Katie M., Lim, Sung Jun, Baird, Michelle A., Stone, John E., Lee, Kwan Young, Davidson, Michael W., Chung, Hee Jung, Schulten, Klaus, Smith, Andrew M., Green, William N., Selvin, Paul R.

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Using VMD: An Introductory Tutorial von Hsin, Jen, Arkhipov, Anton, Yin, Ying, Stone, John E., Schulten, Klaus

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Scalable molecular dynamics on CPU and GPU architectures with NAMD von Phillips, James C., Hardy, David J., Maia, Julio D. C., Stone, John E., Ribeiro, João V., Bernardi, Rafael C., Buch, Ronak, Fiorin, Giacomo, Hénin, Jérôme, Jiang, Wei, McGreevy, Ryan, Melo, Marcelo C. R., Radak, Brian K., Skeel, Robert D., Singharoy, Abhishek, Wang, Yi, Roux, Benoît, Aksimentiev, Aleksei, Luthey-Schulten, Zaida, Kalé, Laxmikant V., Schulten, Klaus, Chipot, Christophe, Tajkhorshid, Emad

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Fast analysis of molecular dynamics trajectories with graphics processing units—Radial distribution function histogramming von Levine, Benjamin G., Stone, John E., Kohlmeyer, Axel

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Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism von Singharoy, Abhishek, Maffeo, Christopher, Delgado-Magnero, Karelia H., Swainsbury, David J.K., Sener, Melih, Kleinekathöfer, Ulrich, Vant, John W., Nguyen, Jonathan, Hitchcock, Andrew, Isralewitz, Barry, Teo, Ivan, Chandler, Danielle E., Stone, John E., Phillips, James C., Pogorelov, Taras V., Mallus, M. Ilaria, Chipot, Christophe, Luthey-Schulten, Zaida, Tieleman, D. Peter, Hunter, C. Neil, Tajkhorshid, Emad, Aksimentiev, Aleksei, Schulten, Klaus

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Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations von Hallock, Michael J., Stone, John E., Roberts, Elijah, Fry, Corey, Luthey-Schulten, Zaida

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Dynamics of chromosome organization in a minimal bacterial cell von Gilbert, Benjamin R, Thornburg, Zane R, Brier, Troy A, Stevens, Jan A, Grünewald, Fabian, Stone, John E, Marrink, Siewert J, Luthey-Schulten, Zaida

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py-MCMD: Python Software for Performing Hybrid Monte Carlo/Molecular Dynamics Simulations with GOMC and NAMD von Barhaghi, Mohammad Soroush, Crawford, Brad, Schwing, Gregory, Hardy, David J., Stone, John E., Schwiebert, Loren, Potoff, Jeffrey, Tajkhorshid, Emad

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VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations von Spivak, Mariano, Stone, John E., Ribeiro, João, Saam, Jan, Freddolino, Peter L., Bernardi, Rafael C., Tajkhorshid, Emad

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Accelerating molecular modeling applications with graphics processors von Stone, John E, Phillips, James C, Freddolino, Peter L, Hardy, David J, Trabuco, Leonardo G, Schulten, Klaus

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