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William Humphrey, Andrew Dalke, and Klaus Schulten.
VMD - Visual Molecular Dynamics.
J. Mol. Graphics, 14:33-38, 1996.

R. Sharma, T. S. Huang, V. I. Pavlovic, K. Schulten, A. Dalke, J. Phillips, M. Zeller, W. Humphrey, Y. Zhao, Z. Lo, and S. Chu.
Speech/gesture interface to a visual computing environment for molecular biologists.
In Proceedings of 13th ICPR 96, volume 3, pages 964-968, 1996.

Rajeev Sharma, Michael Zeller, Vladimir I. Pavlovic, Thomas S. Huang, Zion Lo, Stephen Chu, Yunxin Zhao, James C. Phillips, and Klaus Schulten.
Speech/gesture interface to a visual-computing environment.
IEEE Comp. Graph. App., 20:29-37, 2000.

Simon Cross, Michelle M. Kuttell, John E. Stone, and James E. Gain.
Visualization of cyclic and multi-branched molecules with VMD.
J. Mol. Graph. Model., 28:131-139, 2009.

John E. Stone, Axel Kohlmeyer, Kirby L. Vandivort, and Klaus Schulten.
Immersive molecular visualization and interactive modeling with commodity hardware.
Lect. Notes in Comp. Sci., 6454:382-393, 2010.

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
Immersive out-of-core visualization of large-size and long-timescale molecular dynamics trajectories.
Lect. Notes in Comp. Sci., 6939:1-12, 2011.

John E. Stone, William R. Sherman, and Klaus Schulten.
Immersive molecular visualization with omnidirectional stereoscopic ray tracing and remote rendering.
2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pages 1048-1057, 2016.

Michael Zeller, James C. Phillips, Andrew Dalke, William Humphrey, Klaus Schulten, Rajeev Sharma, T. S. Huang, V. I. Pavlovic, Y. Zhao, Z. Lo, and S. Chu.
A visual computing environment for very large scale biomolecular modeling.
In Proceedings of the 1997 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), pages 3-12. IEEE Computer Society Press, 1997.

John E. Stone, Justin Gullingsrud, Paul Grayson, and Klaus Schulten.
A system for interactive molecular dynamics simulation.
In John F. Hughes and Carlo H. Séquin, editors, 2001 ACM Symposium on Interactive 3D Graphics, pages 191-194, New York, 2001. ACM SIGGRAPH.

Matthieu Chavent, Tyler Reddy, Joseph Goose, Anna Caroline E. Dahl, John E. Stone, Bruno Jobard, and Mark S.P. Sansom.
Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.
Faraday Discuss., 169:455-475, 2014.

Benjamin G. Levine, John E. Stone, and Axel Kohlmeyer.
Fast analysis of molecular dynamics trajectories with graphics processing units-radial distribution function histogramming.
J. Comp. Phys., 230:3556-3569, 2011.

John Stone and Mark Underwood.
Rendering of numerical flow simulations using MPI.
In Second MPI Developer's Conference, pages 138-141. IEEE Computer Society Technical Committee on Distributed Processing, IEEE Computer Society Press, 1996.

John E. Stone.
An Efficient Library for Parallel Ray Tracing and Animation.
Master's thesis, Computer Science Department, University of Missouri-Rolla, April 1998.

John E. Stone, Barry Isralewitz, and Klaus Schulten.
Early experiences scaling VMD molecular visualization and analysis jobs on Blue Waters.
In Extreme Scaling Workshop (XSW), 2013, pages 43-50, Aug. 2013.

I. Wald, G. Johnson, J. Amstutz, C. Brownlee, A. Knoll, J. Jeffers, J. Gunther, and P. Navratil.
OSPRay - a CPU ray tracing framework for scientific visualization.
IEEE Transactions on Visualization and Computer Graphics, 23(1):1-1, 2017.

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten.
Accelerating molecular modeling applications with graphics processors.
J. Comp. Chem., 28:2618-2640, 2007.

John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and James C. Phillips.
GPU computing.
Proc. IEEE, 96:879-899, 2008.

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, and Wen-mei W. Hwu.
GPU acceleration of cutoff pair potentials for molecular modeling applications.
In CF'08: Proceedings of the 2008 conference on Computing Frontiers, pages 273-282, New York, NY, USA, 2008. ACM.

David J. Hardy, John E. Stone, and Klaus Schulten.
Multilevel summation of electrostatic potentials using graphics processing units.
J. Paral. Comp., 35:164-177, 2009.

Volodymyr Kindratenko, Jeremy Enos, Guochun Shi, Michael Showerman, Galen Arnold, John E. Stone, James Phillips, and Wen-mei Hwu.
GPU clusters for high performance computing.
In Cluster Computing and Workshops, 2009. CLUSTER '09. IEEE International Conference on, pages 1-8, 2009.

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, and Klaus Schulten.
GPU-accelerated molecular modeling coming of age.
J. Mol. Graph. Model., 29:116-125, 2010.

John E. Stone, David Gohara, and Guochun Shi.
OpenCL: A parallel programming standard for heterogeneous computing systems.
Comput. in Sci. and Eng., 12:66-73, 2010.

Jeremy Enos, Craig Steffen, Joshi Fullop, Michael Showerman, Guochun Shi, Kenneth Esler, Volodymyr Kindratenko, John E. Stone, and James C. Phillips.
Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters.
In International Conference on Green Computing, pages 317-324, 2010.

John E. Stone, David J. Hardy, Barry Isralewitz, and Klaus Schulten.
GPU algorithms for molecular modeling.
In Jack Dongarra, David A. Bader, and Jakub Kurzak, editors, Scientific Computing with Multicore and Accelerators, chapter 16, pages 351-371. Chapman & Hall/CRC Press, 2011.

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten.
Multilevel summation method for electrostatic force evaluation.
J. Chem. Theor. Comp., 11:766-779, 2015.

John E. Stone, Ryan McGreevy, Barry Isralewitz, and Klaus Schulten.
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.
Faraday Discuss., 169:265-283, 2014.

Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, and Klaus Schulten.
Molecular dynamics-based refinement and validation with Resolution Exchange MDFF for sub-5 Å cryo-electron microscopy maps.
eLife, 10.7554/eLife.16105, 2016.
(66 pages).

John E. Stone, Juan R. Perilla, C. Keith Cassidy, and Klaus Schulten.
GPU-accelerated molecular dynamics clustering analysis with OpenACC.
In Robert Farber, editor, Parallel Programming with OpenACC, pages 215-240. Morgan Kaufmann, Cambridge, MA, 2016.

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, and Klaus Schulten.
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs.
In Proceedings of the 2nd Workshop on General-Purpose Processing on Graphics Processing Units, ACM International Conference Proceeding Series, volume 383, pages 9-18, New York, NY, USA, 2009. ACM.

John E. Stone, David J. Hardy, Jan Saam, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated computation and interactive display of molecular orbitals.
In Wen-mei Hwu, editor, GPU Computing Gems, chapter 1, pages 5-18. Morgan Kaufmann Publishers, 2011.

John E. Stone, Michael J. Hallock, James C. Phillips, Joseph R. Peterson, Zaida Luthey-Schulten, and Klaus Schulten.
Evaluation of emerging energy-efficient heterogeneous computing platforms for biomolecular and cellular simulation workloads.
2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pages 89-100, 2016.

John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms.
Lect. Notes in Comp. Sci., 9945:188-206, 2016.

Michael Krone, John E. Stone, Thomas Ertl, and Klaus Schulten.
Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories.
In EuroVis - Short Papers 2012, pages 67-71, 2012.

Elijah Roberts, John E. Stone, and Zaida Luthey-Schulten.
Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation.
J. Comp. Chem., 34:245-255, 2013.

John E. Stone, Kirby L. Vandivort, and Klaus Schulten.
GPU-accelerated molecular visualization on petascale supercomputing platforms.
In Proceedings of the 8th International Workshop on Ultrascale Visualization, UltraVis '13, pages 6:1-6:8, New York, NY, USA, 2013. ACM.

Melih Sener, John E. Stone, Angela Barragan, Abhishek Singharoy, Ivan Teo, Kirby L. Vandivort, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten.
Visualization of energy conversion processes in a light harvesting organelle at atomic detail.
In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, SC '14. IEEE Press, 2014.

Juan R. Perilla, Boon Chong Goh, John Stone, and Klaus Schulten.
Chemical visualization of human pathogens: the Retroviral Capsids.
Proceedings of the 2015 ACM/IEEE Conference on Supercomputing, 2015.
(4 pages).

John E. Stone, Melih Sener, Kirby L. Vandivort, Angela Barragan, Abhishek Singharoy, Ivan Teo, Joao V. Ribeiro, Barry Isralewitz, Bo Liu, Boon Chong Goh, James C. Phillips, Craig MacGregor-Chatwin, Matthew P. Johnson, Lena F. Kourkoutis, C. Neil Hunter, and Klaus Schulten.
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing.
Parallel Computing, 55:17-27, 2016.

Steven G. Parker, James Bigler, Andreas Dietrich, Heiko Friedrich, Jared Hoberock, David Luebke, David McAllister, Morgan McGuire, Keith Morley, Austin Robison, and Martin Stich.
OptiX: a general purpose ray tracing engine.
In ACM SIGGRAPH 2010 papers, SIGGRAPH '10, pages 66:1-66:13, New York, NY, USA, 2010. ACM.

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Petascale Tcl with NAMD, VMD, and Swift/T.
In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014.

Mark D. Klein and John E. Stone.
Unlocking the full potential of the Cray XK7 accelerator.
In Cray User Group Conf. Cray, May 2014.

John E. Stone, Peter Messmer, Robert Sisneros, and Klaus Schulten.
High performance molecular visualization: In-situ and parallel rendering with EGL.
2016 IEEE International Parallel and Distributed Processing Symposium Workshop (IPDPSW), pages 1014-1023, 2016.

En Cai, Pinghua Ge, Sang Hak Lee, Okunola Jeyifous, Yong Wang, Yanxin Liu, Katie Wilson, Sung Jun Lim, Michelle Baird, John Stone, Kwan Young Lee, Michael Davidson, Hee Jung Chung, Klaus Schulten, Andrew Smith, William Green, and Paul R. Selvin.
Stable small quantum dots for synaptic receptor tracking on live neurons.
Angew. Chem. Int. Ed. Engl., 126:12692-12696, 2014.

Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.
Bioinformatics, page bty761, 2018.

Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, and Alan E. Mark.
Peptide folding: When simulation meets experiment.
Angewandte Chemie International Edition, 38:236-240, 1999.

Laurie J. Heyer, Semyon Kruglyak, and Shibu Yooseph.
Exploring expression data: identification and analysis of coexpressed genes.
Gen. Res., 9:1106-1115, 1999.

Alexander J Bryer, Jodi A Hadden-Perilla, John E Stone, and Juan R Perilla.
High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities.
Journal of chemical information and modeling, 59(10):4328-4338, 2019.

G. Fiorin, M. L. Klein, and J. Hénin.
Using collective variables to drive molecular dynamics simulations.
Mol. Phys., 111(22-23):3345-3362, 2013.

M. Iannuzzi, A. Laio, and M. Parrinello.
Efficient exploration of reactive potential energy surfaces using car-parrinello molecular dynamics.
Phys. Rev. Lett., 90(23):238302, 2003.

E A Coutsias, C Seok, and K A Dill.
Using quaternions to calculate RMSD.
J. Comput. Chem., 25(15):1849-1857, 2004.

Yuguang Mu, Phuong H. Nguyen, and Gerhard Stock.
Energy landscape of a small peptide revealed by dihedral angle principal component analysis.
Proteins, 58(1):45-52, 2005.

Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, and Gerhard Stock.
Dihedral angle principal component analysis of molecular dynamics simulations.
J. Chem. Phys., 126(24):244111, 2007.

Nicholas M Glykos.
Carma: a molecular dynamics analysis program.
J. Comput. Chem., 27(14):1765-1768, 2006.

G. D. Leines and B. Ensing.
Path finding on high-dimensional free energy landscapes.
Phys. Rev. Lett., 109:020601, 2012.

Davide Branduardi, Francesco Luigi Gervasio, and Michele Parrinello.
From a to b in free energy space.
J Chem Phys, 126(5):054103, 2007.

F. Comitani L. Hovan and F. L. Gervasio.
Defining an optimal metric for the path collective variables.
J. Chem. Theory Comput., 15:25-32, 2019.

Marco Jacopo Ferrarotti, Sandro Bottaro, Andrea PĂ©rez-Villa, and Giovanni Bussi.
Accurate multiple time step in biased molecular simulations.
Journal of chemical theory and computation, 11:139-146, 2015.

Reza Salari, Thomas Joseph, Ruchi Lohia, Jérôme Hénin, and Grace Brannigan.
A streamlined, general approach for computing ligand binding free energies and its application to GPCR-bound cholesterol.
Journal of Chemical Theory and Computation, 14(12):6560-6573, 2018.

Eric Darve, David Rodríguez-Gómez, and Andrew Pohorille.
Adaptive biasing force method for scalar and vector free energy calculations.
J. Chem. Phys., 128(14):144120, 2008.

J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.

J. Hénin, G. Fiorin, C. Chipot, and M. L. Klein.
Exploring multidimensional free energy landscapes using time-dependent biases on collective variables.
J. Chem. Theory Comput., 6(1):35-47, 2010.

A. Carter, E, G. Ciccotti, J. T. Hynes, and R. Kapral.
Constrained reaction coordinate dynamics for the simulation of rare events.
Chem. Phys. Lett., 156:472-477, 1989.

M. J. Ruiz-Montero, D. Frenkel, and J. J. Brey.
Efficient schemes to compute diffusive barrier crossing rates.
Mol. Phys., 90:925-941, 1997.

W. K. den Otter.
Thermodynamic integration of the free energy along a reaction coordinate in cartesian coordinates.
J. Chem. Phys., 112:7283-7292, 2000.

Giovanni Ciccotti, Raymond Kapral, and Eric Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.

Adrien Lesage, Tony Lelièvre, Gabriel Stoltz, and Jérôme Hénin.
Smoothed biasing forces yield unbiased free energies with the extended-system adaptive biasing force method.
J. Phys. Chem. B, 121(15):3676-3685, 2017.

A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.

Helmut Grubmüller.
Predicting slow structural transitions in macromolecular systems: Conformational flooding.
Phys. Rev. E, 52(3):2893-2906, Sep 1995.

T. Huber, A. E. Torda, and W.F. van Gunsteren.
Local elevation - A method for improving the searching properties of molecular-dynamics simulation.
Journal of Computer-Aided Molecular Design, 8(6):695-708, DEC 1994.

G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
Phys. Rev. Lett., 96(9):090601, 2006.

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, and Stefano Piana.
A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.
PLOS Computational Biology, 5(8):1-18, 2009.

Yanier Crespo, Fabrizio Marinelli, Fabio Pietrucci, and Alessandro Laio.
Metadynamics convergence law in a multidimensional system.
Phys. Rev. E, 81:055701, May 2010.

Fabrizio Marinelli and José D. Faraldo-Gómez.
Ensemble-biased metadynamics: A molecular simulation method to sample experimental distributions.
Biophysical Journal, 108(12):2779 - 2782, 2015.

Alessandro Barducci, Giovanni Bussi, and Michele Parrinello.
Well-tempered metadynamics: A smoothly converging and tunable free-energy method.
Phys. Rev. Lett., 100:020603, 2008.

P. Raiteri, A. Laio, F. L. Gervasio, C. Micheletti, and M. Parrinello.
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics.
J. Phys. Chem. B, 110(8):3533-9, 2006.

Yuqing Deng and Benoît Roux.
Computations of standard binding free energies with molecular dynamics simulations.
J. Phys. Chem. B, 113(8):2234-2246, 2009.

Jed W. Pitera and John D. Chodera.
On the use of experimental observations to bias simulated ensembles.
J. Chem. Theory Comput., 8:3445-3451, 2012.

A. D. White and G. A. Voth.
Efficient and minimal method to bias molecular simulations with experimental data.
J. Chem. Theory Comput., ASAP, 2014.

Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M Islam, Klaus Schulten, and Benoît Roux.
Structural refinement of proteins by restrained molecular dynamics simulations with non-interacting molecular fragments.
PLoS Comput. Biol., 11(10):e1004368, 2015.