AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.

James C. Phillips

Santiago Antolínez Peter Eugene Jones James C. Phillips Jodi A. Hadden-Perilla AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD. 543-554 2024 64 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.3c01648 db/journals/jcisd/jcisd64.html#AntolinezJPH24

Abigail C. Dommer Lorenzo Casalino Fiona L. Kearns Mia A. Rosenfeld Nicholas Wauer Surl-Hee Ahn John Russo 0003 A. Sofia F. Oliveira Clare Morris Anthony T. Bogetti Anda Trifan Alexander Brace Terra Sztain Austin Clyde Heng Ma S. Chakra Chennubhotla Hyungro Lee Matteo Turilli Syma Khalid Teresa Tamayo-Mendoza Matthew Welborn Anders S. Christensen Daniel G. A. Smith Zhuoran Qiao Sai K. Sirumalla Michael O'Connor Frederick R. Manby Anima Anandkumar David J. Hardy James C. Phillips Abraham C. Stern Josh Romero David Clark Mitchell Dorrell Tom Maiden Lei Huang 0019 John D. McCalpin Christopher J. Woods Alan Gray Matt Williams Bryan Barker Harinda Rajapaksha Richard Pitts Tom Gibbs John E. Stone Daniel M. Zuckerman Adrian J. Mulholland Thomas F. Miller III Shantenu Jha Arvind Ramanathan Lillian T. Chong Rommie E. Amaro #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. 28-44 2023 37 Int. J. High Perform. Comput. Appl. 1 https://doi.org/10.1177/10943420221128233 db/journals/ijhpca/ijhpca37.html#DommerCKRWAROMB23

Anda Trifan Defne Gorgun Michael Salim Zongyi Li Alexander Brace Maxim Zvyagin Heng Ma Austin Clyde David Clark David J. Hardy Tom Burnley Lei Huang 0019 John D. McCalpin Murali Emani Hyenseung Yoo Junqi Yin Aristeidis Tsaris Vishal Subbiah Tanveer Raza Jessica Liu Noah Trebesch Geoffrey Wells Venkatesh Mysore Tom Gibbs James C. Phillips S. Chakra Chennubhotla Ian T. Foster Rick Stevens Anima Anandkumar Venkatram Vishwanath John E. Stone Emad Tajkhorshid Sarah A. Harris Arvind Ramanathan Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action. 603-623 2022 36 Int. J. High Perform. Comput. Appl. 5-6 https://doi.org/10.1177/10943420221113513 db/journals/ijhpca/ijhpca36.html#TrifanGSLBZMCCH22

Lorenzo Casalino Abigail C. Dommer Zied Gaieb Emília P. Barros Terra Sztain Surl-Hee Ahn Anda Trifan Alexander Brace Anthony T. Bogetti Austin Clyde Heng Ma Hyungro Lee Matteo Turilli Syma Khalid Lillian T. Chong Carlos Simmerling David J. Hardy Julio D. C. Maia James C. Phillips Thorsten Kurth Abraham C. Stern Lei Huang 0019 John D. McCalpin Mahidhar Tatineni Tom Gibbs John E. Stone Shantenu Jha Arvind Ramanathan Rommie E. Amaro AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. 2021 35 Int. J. High Perform. Comput. Appl. 5 https://doi.org/10.1177/10943420211006452 db/journals/ijhpca/ijhpca35.html#CasalinoDGBSATB21

Caroline Jay Robert Haines Daniel S. Katz Jeffrey C. Carver Sandra Gesing Steven R. Brandt James Howison Anshu Dubey James C. Phillips Hui Wan Matthew J. Turk The challenges of theory-software translation. 1192 2020 9 F1000Research https://doi.org/10.12688/f1000research.25561.1 https://www.wikidata.org/entity/Q102211508 db/journals/f1000research/f1000research9.html#JayHKCGBHDPWT20

Caroline Jay Robert Haines Daniel S. Katz Jeffrey C. Carver James C. Phillips Anshu Dubey Sandra Gesing Matthew Turk 0002 Hui Wan Hubertus Van Dam James Howison Vitali A. Morozov Steven R. Brandt Theory-Software Translation: Research Challenges and Future Directions. 2019 abs/1910.09902 CoRR http://arxiv.org/abs/1910.09902 db/journals/corr/corr1910.html#abs-1910-09902

Bilge Acun David J. Hardy Laxmikant V. Kalé Keqin Li 0001 James C. Phillips John E. Stone Scalable molecular dynamics with NAMD on the Summit system. 4:1-4:9 2018 62 IBM J. Res. Dev. 6 https://doi.org/10.1147/JRD.2018.2888986 https://www.wikidata.org/entity/Q90184798 db/journals/ibmrd/ibmrd62.html#AcunHKLPS18

James C. Phillips What You Should Know About NAMD and Charm++ But Were Hoping to Ignore. 55:1-55:6 2018 PEARC https://doi.org/10.1145/3219104.3219134 conf/xsede/2018 db/conf/xsede/pearc2018.html#Phillips18

John E. Stone Melih Sener Kirby L. Vandivort Angela M. Barragan Abhishek Singharoy Ivan Teo João V. Ribeiro 0003 Barry Isralewitz Bo Liu Boon Chong Goh James C. Phillips Craig MacGregor-Chatwin Matthew P. Johnson 0002 Lena F. Kourkoutis C. Neil Hunter Klaus Schulten Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing. 17-27 2016 55 Parallel Comput. https://doi.org/10.1016/j.parco.2015.10.015 https://www.wikidata.org/entity/Q36961597 db/journals/pc/pc55.html#StoneSVBSTRILGP16

John E. Stone Michael J. Hallock James C. Phillips Joseph R. Peterson Zaida Luthey-Schulten Klaus Schulten Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads. 89-100 2016 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2016.130 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2016.130 https://www.wikidata.org/entity/Q38831966 conf/ipps/2016w db/conf/ipps/ipdps2016w.html#StoneHPPLS16 John E. Stone Antti-Pekka Hynninen James C. Phillips Klaus Schulten Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms. 188-206 2016 ISC High Performance (Workshops) https://doi.org/10.1007/978-3-319-46079-6_14 https://www.wikidata.org/entity/Q89475641 conf/supercomputer/2016w db/conf/supercomputer/isc2016w.html#StoneHPS16

Wei Jiang James C. Phillips Lei Huang 0019 Mikolai Fajer Yilin Meng James C. Gumbart Yun Luo Klaus Schulten Benoît Roux Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. 908-916 2014 185 Comput. Phys. Commun. 3 https://doi.org/10.1016/j.cpc.2013.12.014 https://www.wikidata.org/entity/Q33763745 db/journals/cphysics/cphysics185.html#JiangPHFMGLSR14

James C. Phillips John E. Stone Kirby L. Vandivort Timothy G. Armstrong Justin M. Wozniak Michael Wilde Klaus Schulten Petascale Tcl with NAMD, VMD, and Swift/T. 6-17 2014 HPTCDL@SC https://doi.org/10.1109/HPTCDL.2014.7 https://doi.ieeecomputersociety.org/10.1109/HPTCDL.2014.7 http://dl.acm.org/citation.cfm?id=2688222 conf/sc/2014hptcdl db/conf/sc/hptcdl2014.html#PhillipsSVAWWS14 James C. Phillips Yanhua Sun Nikhil Jain Eric J. Bohm Laxmikant V. Kalé Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation. 81-91 2014 SC https://doi.org/10.1109/SC.2014.12 https://doi.ieeecomputersociety.org/10.1109/SC.2014.12 https://www.wikidata.org/entity/Q86544696 conf/sc/2014 db/conf/sc/sc2014.html#PhillipsSJBK14 James C. Phillips Klaus Schulten Abhinav Bhatele Chao Mei Yanhua Sun Eric J. Bohm Laxmikant V. Kalé Scalable Molecular Dynamics with NAMD. 61-78 2013 Parallel Science and Engineering Applications books/crc/13/KB2013 db/books/collections/KB2013.html#PhillipsSBMSBK13 Yanhua Sun Gengbin Zheng Chao Mei Eric J. Bohm James C. Phillips Laximant V. Kalé Terry R. Jones Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6. 55 2012 SC https://doi.org/10.1109/SC.2012.87 https://doi.ieeecomputersociety.org/10.1109/SC.2012.87 http://dl.acm.org/citation.cfm?id=2389071 conf/sc/2012 db/conf/sc/sc2012.html#SunZMBPKJ12 Chao Mei Yanhua Sun Gengbin Zheng Eric J. Bohm Laxmikant V. Kalé James C. Phillips Chris Harrison 0001 Enabling and scaling biomolecular simulations of 100 million atoms on petascale machines with a multicore-optimized message-driven runtime. 61:1-61:11 2011 SC https://doi.org/10.1145/2063384.2063466 conf/sc/2011 db/conf/sc/sc2011.html#MeiSZBKPH11 Laxmikant V. Kalé Abhinav Bhatele Eric J. Bohm James C. Phillips NAMD (NAnoscale Molecular Dynamics). 1249-1254 2011 Encyclopedia of Parallel Computing https://doi.org/10.1007/978-0-387-09766-4_505 reference/parallel/2011 db/reference/parallel/parallel2011.html#KaleBBP11 Jeremy Enos Craig P. Steffen Joshi Fullop Michael T. Showerman Guochun Shi Kenneth Esler Volodymyr V. Kindratenko John E. Stone James C. Phillips Quantifying the impact of GPUs on performance and energy efficiency in HPC clusters. 317-324 2010 Green Computing Conference https://doi.org/10.1109/GREENCOMP.2010.5598297 https://doi.ieeecomputersociety.org/10.1109/GREENCOMP.2010.5598297 https://www.wikidata.org/entity/Q106957131 conf/green/2010 db/conf/green/green2010.html#EnosSFSSEKSP10

James C. Phillips John E. Stone Probing biomolecular machines with graphics processors. 34-41 2009 52 Commun. ACM 10 https://doi.org/10.1145/1562764.1562780 https://www.wikidata.org/entity/Q125577458 db/journals/cacm/cacm52.html#PhillipsS09

Praveen K. Chandrasekharan Alexander Kister James C. Phillips Beta-sandwich - beta-barrel transformation may serve as a model of a conversion of 'normal' soluble proteins into amyloid aggregates. 473-489 2009 1 Int. J. Medical Eng. Informatics 4 https://doi.org/10.1504/IJMEI.2009.026814 db/journals/ijmei/ijmei1.html#ChandrasekharanKP09

James C. Phillips John E. Stone Probing Biomolecular Machines with Graphics Processors. 30 2009 7 ACM Queue 9 https://doi.org/10.1145/1626135.1629155 db/journals/queue/queue7.html#PhillipsS09

Guochun Shi Volodymyr V. Kindratenko Ivan S. Ufimtsev Todd J. Martínez James C. Phillips Steven A. Gottlieb Implementation of scientific computing applications on the Cell Broadband Engine. 135-151 2009 17 Sci. Program. 1-2 https://doi.org/10.3233/SPR-2009-0273 db/journals/sp/sp17.html#ShiKUMPG09

Volodymyr V. Kindratenko Jeremy Enos Guochun Shi Michael T. Showerman Galen Wesley Arnold John E. Stone James C. Phillips Wen-mei W. Hwu GPU clusters for high-performance computing. 1-8 2009 CLUSTER https://doi.org/10.1109/CLUSTR.2009.5289128 https://doi.ieeecomputersociety.org/10.1109/CLUSTR.2009.5289128 https://www.wikidata.org/entity/Q106957133 conf/cluster/2009 db/conf/cluster/cluster2009.html#KindratenkoESSASPH09

Sameer Kumar 0001 Chao Huang 0029 Gengbin Zheng Eric J. Bohm Abhinav Bhatele James C. Phillips Hao Yu Laxmikant V. Kalé Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system. 177-188 2008 52 IBM J. Res. Dev. 1-2 https://doi.org/10.1147/rd.521.0177 db/journals/ibmrd/ibmrd52.html#KumarHZBBPYK08

John D. Owens Mike Houston David Luebke Simon Green John E. Stone James C. Phillips GPU Computing. 879-899 2008 96 Proc. IEEE 5 https://doi.org/10.1109/JPROC.2008.917757 https://www.wikidata.org/entity/Q56337884 db/journals/pieee/pieee96.html#OwensHLGSP08

Abhinav Bhatele Sameer Kumar 0001 Chao Mei James C. Phillips Gengbin Zheng Laxmikant V. Kalé Overcoming scaling challenges in biomolecular simulations across multiple platforms. 1-12 2008 IPDPS https://doi.org/10.1109/IPDPS.2008.4536317 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2008.4536317 conf/ipps/2008 db/conf/ipps/ipdps2008.html#BhateleKMPZK08 James C. Phillips John E. Stone Klaus Schulten Adapting a message-driven parallel application to GPU-accelerated clusters. 8 2008 SC https://doi.org/10.1109/SC.2008.5214716 https://dl.acm.org/citation.cfm?id=1413379 conf/sc/2008 db/conf/sc/sc2008.html#PhillipsSS08

John E. Stone James C. Phillips P. L. Freddolino David J. Hardy Leonardo G. Trabuco Klaus Schulten Accelerating molecular modeling applications with graphics processors. 2618-2640 2007 28 J. Comput. Chem. 16 https://doi.org/10.1002/jcc.20829 https://www.wikidata.org/entity/Q34692912 db/journals/jcc/jcc28.html#StonePFHTS07

Robert D. Skeel David J. Hardy James C. Phillips Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations. 1-5 2007 225 J. Comput. Phys. 1 https://doi.org/10.1016/j.jcp.2007.03.010 https://www.wikidata.org/entity/Q43183217 db/journals/jcphy/jcphy225.html#SkeelHP07

David M. Kunzman Gengbin Zheng Eric J. Bohm James C. Phillips Laxmikant V. Kalé Poster reception - Charm++ simplifies coding for the cell processor. 135 2006 conf/sc/2006 SC https://doi.org/10.1145/1188455.1188596 db/conf/sc/sc2006.html#KunzmanZBPK06

James C. Phillips Rosemary Braun Wei Wang 0342 James C. Gumbart Emad Tajkhorshid Elizabeth Villa Christophe Chipot Robert D. Skeel Laxmikant V. Kalé Klaus Schulten Scalable molecular dynamics with NAMD. 1781-1802 2005 26 J. Comput. Chem. 16 https://doi.org/10.1002/jcc.20289 https://www.wikidata.org/entity/Q27860718 db/journals/jcc/jcc26.html#PhillipsBWGTVCSKS05

Gerald Lucovsky James C. Phillips Bond strain and defects at interfaces in high-k gate stacks. 770-778 2005 45 Microelectron. Reliab. 5-6 https://doi.org/10.1016/j.microrel.2004.11.051 db/journals/mr/mr45.html#LucovskyP05

James C. Phillips Gengbin Zheng Sameer Kumar 0001 Laxmikant V. Kalé NAMD: biomolecular simulation on thousands of processors. 53:1-53:18 2002 conf/sc/2002 SC https://doi.org/10.1109/SC.2002.10019 https://doi.ieeecomputersociety.org/10.1109/SC.2002.10019 http://dl.acm.org/citation.cfm?id=762810 db/conf/sc/sc2002.html#PhillipsZKK02

Rajeev Sharma Michael Zeller Vladimir Pavlovic 0001 Thomas S. Huang Zion Lo Stephen M. Chu Yunxin Zhao James C. Phillips Klaus Schulten Speech/Gesture Interface to a Visual-Computing Environment. 29-37 2000 20 IEEE Computer Graphics and Applications 2 https://doi.org/10.1109/38.824531 http://doi.ieeecomputersociety.org/10.1109/38.824531 db/journals/cga/cga20.html#SharmaZPHLCZPS00

Robert Brunner James C. Phillips Laxmikant V. Kalé Scalable Molecular Dynamics for Large Biomolecular Systems. 2000 conf/sc/2000 SC https://doi.org/10.1109/SC.2000.10038 https://doi.ieeecomputersociety.org/10.1109/SC.2000.10038 http://dl.acm.org/citation.cfm?id=370448 db/conf/sc/sc2000.html#BrunnerPK00 45 Laxmikant V. Kalé Robert Brunner James C. Phillips Krishnan Varadarajan Application Performance of a Linux Cluster Using Converse. 483-495 1999 conf/ipps/1999w IPPS/SPDP Workshops db/conf/ipps/ippsw1999.html#KaleBPV99 https://doi.org/10.1007/BFb0097933 James C. Phillips Robert Brunner Aritomo Shinozaki Milind A. Bhandarkar Neal Krawetz Attila Gürsoy Laxmikant V. Kalé Robert D. Skeel Klaus Schulten Avoiding Algorithmic Obfuscation in a Message-Driven Parallel MD Code. 472-482 1999 Computational Molecular Dynamics https://doi.org/10.1007/978-3-642-58360-5_28 books/sp/99/DHLM1999 db/books/collections/DHLM1999.html#PhillipsBSBKGKSS99

James C. Phillips Algebraic Constructs for the Graphical and Computational Solution to Balancing Chemical Equations. 295-308 1998 22 Comput. Chem. 4 https://doi.org/10.1016/S0097-8485(97)00066-1 db/journals/candc/candc22.html#Phillips98

Michael Zeller James C. Phillips Andrew Dalke William Humphrey Klaus Schulten Thomas S. Huang Vladimir Pavlovic 0001 Yunxin Zhao Zion Lo Stephen M. Chu Rajeev Sharma A Visual Computing Environment for Very Large Scale Biomolecular Modeling. 3- 1997 conf/asap/1997 ASAP https://doi.org/10.1109/ASAP.1997.606807 https://doi.ieeecomputersociety.org/10.1109/ASAP.1997.606807 https://www.wikidata.org/entity/Q114799811 db/conf/asap/asap1997.html#ZellerPDHSHPZLCS97 Laxmikant V. Kalé Milind A. Bhandarkar Robert Brunner Neal Krawetz James C. Phillips Aritomo Shinozaki NAMD: A Case Study in Multilingual Parallel Programming. 367-381 1997 conf/lcpc/1997 LCPC db/conf/lcpc/lcpc1997.html#KaleBBKPS97 https://doi.org/10.1007/BFb0032705 Bilge Acun Surl-Hee Ahn Rommie E. Amaro Anima Anandkumar Santiago Antolínez Timothy G. Armstrong Galen Wesley Arnold Bryan Barker Angela M. Barragan Emília P. Barros Milind A. Bhandarkar Abhinav Bhatele Anthony T. Bogetti Eric J. Bohm Alex BraceAlexander Brace Steven R. Brandt Rosemary Braun Robert Brunner Tom Burnley Jeffrey C. Carver Lorenzo Casalino Praveen K. Chandrasekharan S. Chakra Chennubhotla Christophe Chipot Lillian T. Chong Anders S. Christensen Stephen M. Chu David Clark Austin Clyde Andrew Dalke Huub J. J. Van DamHubertus Van Dam Abigail C. Dommer Mitchell Dorrell Anshu Dubey Murali Emani Jeremy Enos Kenneth Esler Mikolai Fajer Ian T. Foster Lydia FreddolinoP. L. Freddolino Joshi Fullop Zied Gaieb Sandra Gesing Tom Gibbs Boon Chong Goh Defne Gorgun Steven A. Gottlieb Alan Gray Simon Green James C. Gumbart Attila Gürsoy Jodi A. Hadden-Perilla Robert Haines Michael J. Hallock David J. Hardy Sarah A. Harris Chris Harrison 0001 Mike Houston James Howison Chao Huang 0029 Lei Huang 0019 Thomas S. Huang William Humphrey C. Neil Hunter Wen-Mei W. HwuWen-mei W. Hwu Antti-Pekka Hynninen Barry Isralewitz Nikhil Jain Caroline Jay Shantenu Jha Wei Jiang Matthew P. Johnson 0002 Peter Eugene Jones Terry R. Jones Laximant V. Kalé Laxmikant V. Kalé Daniel S. Katz Fiona L. Kearns Syma Khalid Volodymyr V. Kindratenko Alexander Kister Lena F. Kourkoutis Neal Krawetz Sameer Kumar 0001 David M. Kunzman Thorsten Kurth Hyungro Lee Keqin Li 0001 Zongyi Li Bo Liu Jessica Liu Zion Lo Gerald Lucovsky David P. LuebkeDavid Luebke Yun Luo Zaida Luthey-Schulten Heng Ma Craig MacGregor-Chatwin Julio D. C. Maia Tom Maiden Frederick R. Manby Todd J. Martínez John D. McCalpin Chao Mei Yilin Meng Thomas F. Miller III Vitali A. Morozov Clare Morris Adrian J. Mulholland Venkatesh Mysore Michael O'Connor A. Sofia F. Oliveira John D. Owens Vladimir Pavlovic 0001 Joseph R. Peterson Richard Pitts Zhuoran Qiao Harinda Rajapaksha Arvind Ramanathan Tanveer Raza João Ribeiro 0003João V. Ribeiro 0003 Josh Romero Mia A. Rosenfeld Benoît Roux John Russo 0003 Michael Salim Klaus Schulten Melih Sener Rajeev Sharma Guochun Shi Aritomo Shinozaki Michael T. Showerman Carlos Simmerling Abhishek Singharoy Sai K. Sirumalla Robert D. Skeel Daniel G. A. Smith Craig P. Steffen Abraham C. Stern Rick L. StevensRick Stevens John E. Stone Vishal Subbiah Yanhua Sun Terra Sztain Emad Tajkhorshid Teresa Tamayo-Mendoza Mahidhar Tatineni Ivan Teo Leonardo G. Trabuco Noah Trebesch Anda Trifan Aristeidis Tsaris Matteo Turilli Matthew J. TurkMatthew Turk 0002 Ivan S. Ufimtsev Kirby L. Vandivort Krishnan Varadarajan Elizabeth Villa Venkatram Vishwanath Hui Wan Wei Wang 0342 Nicholas Wauer Matthew Welborn Geoffrey Wells Michael Wilde Matt Williams Christopher J. Woods Justin M. Wozniak Junqi Yin Hyenseung Yoo Hao Yu Michael Zeller Yunxin Zhao Gengbin Zheng Daniel M. Zuckerman Maxim Zvyagin