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Index
- 1
-
William Humphrey, Andrew Dalke, and Klaus Schulten.
VMD - Visual Molecular Dynamics.
J. Mol. Graphics, 14:33-38, 1996.
- 2
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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.
- 3
-
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.
- 4
-
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.
- 5
-
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.
- 6
-
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.
- 7
-
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.
- 8
-
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.
- 9
-
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.
- 10
-
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.
- 11
-
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.
- 12
-
John E. Stone.
An Efficient Library for Parallel Ray Tracing and Animation.
Master's thesis, Computer Science Department, University of
Missouri-Rolla, April 1998.
- 13
-
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.
- 14
-
John D. Owens, Mike Houston, David Luebke, Simon Green, John E. Stone, and
James C. Phillips.
GPU computing.
Proc. IEEE, 96:879-899, 2008.
- 15
-
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.
- 16
-
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.
- 17
-
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.
- 18
-
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.
- 19
-
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.
- 20
-
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.
- 21
-
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.
- 22
-
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.
- 23
-
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.
- 24
-
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.
- 25
-
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.
- 26
-
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.
- 27
-
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.
- 28
-
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.
- 29
-
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.
- 30
-
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.
- 31
-
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.
- 32
-
G. Fiorin, M. L. Klein, and J. Hénin.
Using collective variables to drive molecular dynamics simulations.
Mol. Phys., 111(22-23):3345-3362, 2013.
- 33
-
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.
- 34
-
E A Coutsias, C Seok, and K A Dill.
Using quaternions to calculate RMSD.
J. Comput. Chem., 25(15):1849-1857, 2004.
- 35
-
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.
- 36
-
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.
- 37
-
Nicholas M Glykos.
Carma: a molecular dynamics analysis program.
J. Comput. Chem., 27(14):1765-1768, 2006.
- 38
-
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.
- 39
-
J. Hénin and C. Chipot.
Overcoming free energy barriers using unconstrained molecular
dynamics simulations.
J. Chem. Phys., 121:2904-2914, 2004.
- 40
-
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.
- 41
-
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.
- 42
-
M. J. Ruiz-Montero, D. Frenkel, and J. J. Brey.
Efficient schemes to compute diffusive barrier crossing rates.
Mol. Phys., 90:925-941, 1997.
- 43
-
W. K. den Otter.
Thermodynamic integration of the free energy along a reaction
coordinate in cartesian coordinates.
J. Chem. Phys., 112:7283-7292, 2000.
- 44
-
Giovanni Ciccotti, Raymond Kapral, and Eric Vanden-Eijnden.
Blue moon sampling, vectorial reaction coordinates, and unbiased
constrained dynamics.
ChemPhysChem, 6(9):1809-1814, 2005.
- 45
-
A. Laio and M. Parrinello.
Escaping free-energy minima.
Proc. Natl. Acad. Sci. USA, 99(20):12562-12566, 2002.
- 46
-
Helmut Grubmüller.
Predicting slow structural transitions in macromolecular systems:
Conformational flooding.
Phys. Rev. E, 52(3):2893-2906, Sep 1995.
- 47
-
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.
- 48
-
G. Bussi, A. Laio, and M. Parrinello.
Equilibrium free energies from nonequilibrium metadynamics.
Phys. Rev. Lett., 96(9):090601, 2006.
- 49
-
Alessandro Barducci, Giovanni Bussi, and Michele Parrinello.
Well-tempered metadynamics: A smoothly converging and tunable
free-energy method.
Phys. Rev. Lett., 100:020603, 2008.
- 50
-
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, 2005.
- 51
-
Yuqing Deng and Benoît Roux.
Computations of standard binding free energies with molecular
dynamics simulations.
J. Phys. Chem. B, 113(8):2234-2246, 2009.
- 52
-
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.
- 53
-
A. D. White and G. A. Voth.
Efficient and minimal method to bias molecular simulations with
experimental data.
J. Chem. Theory Comput., ASAP, 2014.
vmd@ks.uiuc.edu