Recent Developments in Amber Biomolecular Simulations.

Thomas E. Cheatham Thomas E. Cheatham III http://home.chpc.utah.edu/~cheatham/

David A. Case David S. Cerutti Vinícius Wilian D. Cruzeiro Thomas A. Darden Robert E. Duke Mahdieh Ghazimirsaeed George M. Giambasu Timothy J. Giese Andreas W. Götz Julie A. Harris Koushik Kasavajhala Tai-Sung Lee Zhen Li 0038 Charles Lin Jian Liu 0019 Yinglong Miao Romelia Salomón-Ferrer Jana Shen Ryan Snyder Jason M. Swails Ross C. Walker Jinan Wang Xiongwu Wu Jinzhe Zeng Thomas E. Cheatham III Daniel R. Roe Adrian E. Roitberg Carlos Simmerling Darrin M. York Maria C. Nagan Kenneth M. Merz Jr. Recent Developments in Amber Biomolecular Simulations. 7835-7843 2025 65 J. Chem. Inf. Model. 15 https://doi.org/10.1021/acs.jcim.5c01063 db/journals/jcisd/jcisd65.html#CaseCCDDGGGGHKLLLLMSSSS25 streams/journals/jcisd

Lauren Winkler Thomas E. Cheatham Benchmarking the Drude Polarizable Force Field Using the r(GACC) Tetranucleotide. 2505-2511 2023 April 63 J. Chem. Inf. Model. 8 https://doi.org/10.1021/acs.jcim.3c00250 db/journals/jcisd/jcisd63.html#WinklerC23

David A. Case Hasan Metin Aktulga Kellon Belfon David S. Cerutti G. Andrés Cisneros Vinícius Wilian D. Cruzeiro Negin Forouzesh Timothy J. Giese Andreas W. Götz Holger Gohlke Saeed Izadi Koushik Kasavajhala Mehmet Cagri Kaymak Edward King Tom Kurtzman Tai-Sung Lee Pengfei Li 0003 Jian Liu 0019 Tyler Luchko Ray Luo 0001 Madushanka Manathunga Matías R. Machado Hai Minh Nguyen Kurt A. O'Hearn Alexey V. Onufriev Feng Pan Sergio Pantano Ruxi Qi Ali Rahnamoun Ali Risheh Stephan Schott-Verdugo Akhil Shajan Jason M. Swails Junmei Wang Haixin Wei Xiongwu Wu Yongxian Wu Shi Zhang Shiji Zhao Qiang Zhu Thomas E. Cheatham Daniel R. Roe Adrian E. Roitberg Carlos Simmerling Darrin M. York Maria C. Nagan Kenneth M. Merz Jr. AmberTools. 6183-6191 2023 October 63 J. Chem. Inf. Model. 20 https://doi.org/10.1021/acs.jcim.3c01153 db/journals/jcisd/jcisd63.html#CaseABCCCFGGGIKKKKLLLLLMMNOOPPQRR23

Joel Cutcher-Gershenfeld Torey Battelle Dana Brunson Thomas E. Cheatham Jacob Fosso-Tande Douglas M. Jennewein Julie Ma Lauren A. Michael Timothy Middelkoop Henry Neeman Patrick Schmitz Professionalization of Research Computing and Data: An Expanded Agenda. 129-136 2023 PEARC https://doi.org/10.1145/3569951.3593610 conf/xsede/2023 db/conf/xsede/pearc2023.html#Cutcher-Gershenfeld23 Thomas J. Hacker Preston M. Smith Dana Brunson Lisa Arafune Thomas E. Cheatham Ewa Deelman Building the Research Innovation Workforce: Challenges and Recommendations from a Virtual Workshop to Advance the Research Computing Community✱. 26:1-26:7 2022 PEARC https://doi.org/10.1145/3491418.3530288 conf/xsede/2022 db/conf/xsede/pearc2022.html#HackerSBACD22

Patrick Schmitz Scott Yockel Claire Mizumoto Thomas E. Cheatham Dana Brunson Advancing the Workforce That Supports Computationally and Data Intensive Research. 19-27 2021 23 Comput. Sci. Eng. 5 https://doi.org/10.1109/MCSE.2021.3098421 https://www.wikidata.org/entity/Q113311989 db/journals/cse/cse23.html#SchmitzYMCB21

Julie Ma Sarah Akbar Torey Battelle Kevin L. Brandt Eric Brown Dana Brunson Dhruva Chakravorty Thomas E. Cheatham Bhushan Chitre Adrian Del Maestro Andrea Elledge Vikram Gazula John Goodhue James Griffioen Abigail Hyde Douglas M. Jennewein Shelley Knuth B. J. Lougee Timothy Middelkoop Sasmita Mohapatra Sia Najafi Kaylea Nelson Lisa Perez Bruce Segee Julia Sheats Andrew H. Sherman Christopher Simmons Ermal Toto Scott A. Valcourt Lucas Varella Ralph Zottola The Connect.Cyberinfrastructure Portal. 51:1-51:4 2021 PEARC https://doi.org/10.1145/3437359.3465606 conf/xsede/2021 db/conf/xsede/pearc2021.html#MaABBBBCCCMEGGG21 Patrick Schmitz Dana Brunson Gail Krovitz Thomas E. Cheatham Claire Mizumoto Leveraging a research computing and data capabilities model for strategic decision-making. 12:1 2020 PEARC Companion https://doi.org/10.1145/3425306.3444807 conf/xsede/2020c db/conf/xsede/pearc2020c.html#SchmitzBKCM20 Patrick Schmitz Claire Mizumoto John Hicks Dana Brunson Gail Krovitz James B. Bottum Joel Cutcher-Gershenfeld Karen Wetzel Thomas E. Cheatham A Research Computing and Data Capabilities Model for Strategic Decision-Making. 77-84 2020 PEARC https://doi.org/10.1145/3311790.3396643 conf/xsede/2020 db/conf/xsede/pearc2020.html#SchmitzMHBKBCWC20 Sharon Broude Geva Dana Brunson Thomas E. Cheatham III James Deaton James Griffioen Curtis W. Hillegas Douglas M. Jennewein Gail Krovitz Tobin Magle Patrick Schmitz Karen Tomko James C. Wilgenbusch Fostering Collaboration Among Organizations in the Research Computing and Data Ecosystem. 393-401 2020 PEARC https://doi.org/10.1145/3311790.3396645 conf/xsede/2020 db/conf/xsede/pearc2020.html#GevaBCDGHJKMSTW20 Craig A. Stewart David Y. Hancock Julie Wernert Thomas R. Furlani David Lifka Alan Sill Nicholas Berente Donald F. McMullen Thomas E. Cheatham Amy W. Apon Ron Payne Shawn D. Slavin Assessment of financial returns on investments in cyberinfrastructure facilities: A survey of current methods. 33:1-33:8 2019 PEARC https://doi.org/10.1145/3332186.3332228 conf/xsede/2019 db/conf/xsede/pearc2019.html#StewartHWFLSBMC19 Andrew J. Monaghan Brett Milash Tobin Magle Thomas Hauser Thomas E. Cheatham Patrick J. Burns 0002 Shelley Knuth Anita M. Orendt Suzi White Dawn Paschal Howard Jay Siegel Timothy Kaiser Andrew M. Johnson 0002 Becky Yeager Improving regional cyberinfrastructure services through collaboration: Cyberteam for the Rocky Mountain Advanced Computing Consortium. 41:1-41:4 2019 PEARC https://doi.org/10.1145/3332186.3332232 https://www.wikidata.org/entity/Q122386718 conf/xsede/2019 db/conf/xsede/pearc2019.html#MonaghanMMHCBKO19

Daniel R. Roe Thomas E. Cheatham III Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data. 2110-2117 2018 39 J. Comput. Chem. 25 https://doi.org/10.1002/jcc.25382 https://www.wikidata.org/entity/Q58126150 db/journals/jcc/jcc39.html#RoeC18

Ioannis Paraskevakos André Luckow Mahzad Khoshlessan George Chantzialexiou Thomas E. Cheatham Oliver Beckstein Geoffrey C. Fox Shantenu Jha Task-parallel Analysis of Molecular Dynamics Trajectories. 49:1-49:10 2018 ICPP https://doi.org/10.1145/3225058.3225128 https://www.wikidata.org/entity/Q131121092 conf/icpp/2018 db/conf/icpp/icpp2018.html#ParaskevakosLKC18

Marie Zgarbová Petr Jurecka Filip Lankas Thomas E. Cheatham III Jirí Sponer Michal Otyepka Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. 275-287 2017 57 J. Chem. Inf. Model. 2 https://doi.org/10.1021/acs.jcim.6b00621 https://www.wikidata.org/entity/Q38774124 db/journals/jcisd/jcisd57.html#ZgarbovaJLCSO17

Amit Roy Daniel R. Roe Mary W. Hall Thomas E. Cheatham Polyhedral Compilation Support for C++ Features: A Case Study with CPPTRAJ. 26-35 2017 LCPC https://doi.org/10.1007/978-3-030-35225-7_3 conf/lcpc/2017 db/conf/lcpc/lcpc2017.html#RoyRHC17

Zahra Heidari Daniel R. Roe Rodrigo Galindo-Murillo Jahan B. Ghasemi Thomas E. Cheatham III Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations. 1282-1291 2016 56 J. Chem. Inf. Model. 7 https://doi.org/10.1021/acs.jcim.5b00727 https://www.wikidata.org/entity/Q39693279 db/journals/jcisd/jcisd56.html#HeidariRGGC16

Thomas E. Cheatham III Daniel R. Roe The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis. 30-39 2015 17 Comput. Sci. Eng. 2 https://doi.org/10.1109/MCSE.2015.7 http://doi.ieeecomputersociety.org/10.1109/MCSE.2015.7 https://www.wikidata.org/entity/Q113312743 db/journals/cse/cse17.html#CheathamR15

Julien C. Thibault Daniel R. Roe Julio C. Facelli Thomas E. Cheatham III Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing. 4 2014 6 J. Cheminformatics 1 https://doi.org/10.1186/1758-2946-6-4 https://www.wikidata.org/entity/Q30746483 db/journals/jcheminf/jcheminf6.html#ThibaultRFC14

Niel M. Henriksen Hamed S. Hayatshahi Darrell R. Davis Thomas E. Cheatham III Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations. 1758-1772 2014 54 J. Chem. Inf. Model. 6 https://doi.org/10.1021/ci500132c https://www.wikidata.org/entity/Q30582034 db/journals/jcisd/jcisd54.html#HenriksenHDC14

Julien C. Thibault Thomas E. Cheatham III Julio C. Facelli iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. 1810-1819 2014 54 J. Chem. Inf. Model. 6 https://doi.org/10.1021/ci500173w https://www.wikidata.org/entity/Q30821313 db/journals/jcisd/jcisd54.html#ThibaultCCF14

Julien C. Thibault Julio C. Facelli Thomas E. Cheatham III iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment. 726-736 2013 53 J. Chem. Inf. Model. 3 https://doi.org/10.1021/ci300524j https://www.wikidata.org/entity/Q30589155 db/journals/jcisd/jcisd53.html#ThibaultFC13

Kiumars Shahrokh Anita M. Orendt Garold S. Yost Thomas E. Cheatham III Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. 119-133 2012 33 J. Comput. Chem. 2 https://doi.org/10.1002/jcc.21922 https://www.wikidata.org/entity/Q31035806 db/journals/jcc/jcc33.html#ShahrokhOYC12

Niel M. Henriksen Thomas E. Cheatham III RNA structure refinement and force field evaluation using molecular dynamics simulations. 3:1 2011 TG https://doi.org/10.1145/2016741.2016745 conf/tg/2011 db/conf/tg/tg2011.html#HenriksenC11

Thanh N. Truong Manohar Nayak Hung H. Huynh Tom Cook Priya Mahajan Le-Thuy T. Tran Jannu Bharath Shrish Jain Ha B. Pham Chaiwoot Boonyasiriwat Nhat Nguyen Evan Andersen Yong Kim Suengkeol Choe Jihoon Choi Thomas E. Cheatham III Julio C. Facelli Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure for Scientific Computing. 971-984 2006 46 J. Chem. Inf. Model. 3 https://doi.org/10.1021/ci0503917 https://www.wikidata.org/entity/Q38453110 db/journals/jcisd/jcisd46.html#TruongNHCMTBJPBNAKCCCF06

David A. Case Thomas E. Cheatham III Tom Darden Holger Gohlke Ray Luo 0001 Kenneth M. Merz Jr. Alexey Onufriev Carlos Simmerling Bing Wang Robert J. Woods The Amber biomolecular simulation programs. 1668-1688 2005 26 J. Comput. Chem. 16 https://doi.org/10.1002/jcc.20290 https://www.wikidata.org/entity/Q27860745 db/journals/jcc/jcc26.html#CaseCDGLMOSWW05

Stephen C. Harvey Robert K.-Z. Tan Thomas E. Cheatham III The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition. 726-740 1998 19 J. Comput. Chem. 7 https://doi.org/10.1002/(SICI)1096-987X(199805)19:7<726::AID-JCC4>3.0.CO;2-S db/journals/jcc/jcc19.html#HarveyTC98

Michael F. Crowley Thomas A. Darden Thomas E. Cheatham III David W. Deerfield II Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program. 255-278 1997 11 J. Supercomput. 3 https://doi.org/10.1023/A:1007907925007 db/journals/tjs/tjs11.html#CrowleyDCD97

Thomas A. Darden Lee G. Pedersen Abdulnour Y. Toukmaji Michael F. Crowley Thomas E. Cheatham Particle-Mesh Based Methods for Fast Ewald Summation in Molecular Dynamics Simulations. 1997 conf/ppsc/1997 PP db/conf/ppsc/ppsc1997.html#DardenPTCC97 Thomas E. Cheatham Amr F. Fahmy Dan C. Stefanescu Leslie G. Valiant Bulk synchronous parallel computing-a paradigm for transportable software. 268-275 1995 conf/hicss/1995 HICSS (2) https://doi.org/10.1109/HICSS.1995.375451 https://doi.ieeecomputersociety.org/10.1109/HICSS.1995.375451 db/conf/hicss/hicss1995.html#CheathamFSV95 Thomas E. Cheatham Amr F. Fahmy Dan C. Stefanescu General Purpose Optimization Technology. 422-433 1995 conf/lcpc/1995 LCPC db/conf/lcpc/lcpc1995.html#CheathamFS95 https://doi.org/10.1007/BFb0014215 Thomas E. Cheatham Haiming Gao Dan C. Stefanescu A Suite of Analysis Tools Based on a General Purpose Abstract Interpreter. 188-202 1994 conf/cc/1994 CC db/conf/cc/cc94.html#CheathamGS94 https://doi.org/10.1007/3-540-57877-3_13 Thomas E. Cheatham Amr F. Fahmy Dan C. Stefanescu H-BSP - A General Purpose Parallel Computing Environment. 515-520 1994 conf/ifip/1994-1 IFIP Congress (1) db/conf/ifip/ifip94-1.html#CheathamFS94 Thomas E. Cheatham Amr F. Fahmy Dan C. Stefanescu Supporting multiple evolving compilers. 241-248 1994 conf/seke/1994 SEKE db/conf/seke/seke1994.html#CheathamFS94 Geoffrey C. Fox Sanjay Ranka Michael L. Scott Allen D. Malony James C. Browne Marina C. Chen Alok N. Choudhary Thomas E. Cheatham Janice E. Cuny Rudolf Eigenmann Amr F. Fahmy Ian T. Foster Dennis Gannon Tomasz Haupt Carl Kesselman Charles Koelbel Wei Li 0015 Monica S. Lam Thomas J. LeBlanc Jim Openshaw David A. Padua Constantine D. Polychronopoulos Joel H. Saltz Alan Sussman Gil Weigand Katherine A. Yelick Common runtime support for high-performance parallel languages. 752-757 1993 conf/sc/1993 SC https://doi.org/10.1145/169627.169826 https://doi.ieeecomputersociety.org/10.1109/SUPERC.1993.1263529 db/conf/sc/sc1993.html#FoxRSMBCCCCEFFGHKKLLLOPPSSWY93 Thomas E. Cheatham Dan C. Stefanescu A Suite of Optimizers Based on Abstract Interpretation. 75-81 1992 conf/pepm/1992 PEPM db/conf/pepm/pepm92.html#CheathamS92 Azer Bestavros Thomas E. Cheatham Efficient Execution of Homogeneous Tasks with Unequal Run Times on the Connection Machine. 304-305 1991 conf/icpp/1991-3 ICPP (3) db/conf/icpp/icpp1991-3.html#BestavrosC91 Azer Bestavros Thomas E. Cheatham Dan C. Stefanescu Parallel bin packing using first fit and k-delayed best-fit heuristics. 501-504 1990 conf/spdp/1990 SPDP https://doi.org/10.1109/SPDP.1990.143591 https://doi.ieeecomputersociety.org/10.1109/SPDP.1990.143591 https://www.wikidata.org/entity/Q61693879 db/conf/spdp/spdp90.html#BestavrosCS90

Thomas E. Cheatham Compiling techniques. 481 1966 9 Commun. ACM 7 https://doi.org/10.1145/365719.366426 db/journals/cacm/cacm9.html#Cheatham66

Sarah Akbar Hasan Metin Aktulga Evan Andersen Amy W. Apon Lisa Arafune Torey Battelle Oliver Beckstein Kellon Belfon Nicholas Berente Azer Bestavros Jannu Bharath Chaiwoot Boonyasiriwat James B. Bottum Kevin L. Brandt Eric Brown James C. Browne Dana Brunson Patrick J. Burns 0002 David A. Case David S. Cerutti Dhruva Chakravorty George Chantzialexiou Marina C. Chen Bhushan Chitre Suengkeol Choe Jihoon Choi Alok N. Choudhary G. Andrés Cisneros Tom Cook Michael F. Crowley Vinícius Wilian D. Cruzeiro Janice E. Cuny Joel Cutcher-Gershenfeld Thomas A. DardenTom Darden Darrell R. Davis James Deaton Ewa Deelman David W. Deerfield II Robert E. Duke Rudolf Eigenmann Andrea Elledge Julio C. Facelli Amr F. Fahmy Negin Forouzesh Jacob Fosso-Tande Ian T. Foster Geoffrey C. Fox Thomas R. Furlani Rodrigo Galindo-Murillo Dennis Gannon Haiming Gao Vikram Gazula Sharon Broude Geva Jahan B. Ghasemi Mahdieh Ghazimirsaeed George M. Giambasu Timothy J. Giese Holger Gohlke John Goodhue Andreas W. Götz Jim GriffioenJames Griffioen Thomas J. Hacker Mary W. Hall David Y. Hancock Julie A. Harris Stephen C. Harvey Tomasz Haupt Thomas Hauser Hamed S. Hayatshahi Zahra Heidari Niel M. Henriksen John Hicks Curtis W. Hillegas Hung H. Huynh Abigail Hyde Saeed Izadi Shrish Jain Douglas M. Jennewein Shantenu Jha Andrew M. Johnson 0002 Petr Jurecka Timothy Kaiser Koushik Kasavajhala Mehmet Cagri Kaymak Carl Kesselman Mahzad Khoshlessan Yong Kim Edward King Shelley Knuth Charles Koelbel Gail Krovitz Tom Kurtzman Monica S. Lam Filip Lankas Thomas J. LeBlanc Tai-Sung Lee Pengfei Li 0003 Wei Li 0015 Zhen Li 0038 David Lifka Charles Lin Jian Liu 0019 B. J. Lougee Tyler Luchko André Luckow Ray Luo 0001 Julie Ma Matías R. Machado Adrian Del Maestro Tobin Magle Priya Mahajan Allen D. Malony Madushanka Manathunga Donald F. McMullen Kenneth M. Merz Jr. Yinglong Miao Lauren A. Michael Timothy Middelkoop Brett Milash Claire Mizumoto Sasmita Mohapatra Andrew J. Monaghan Maria C. Nagan Sia Najafi Manohar Nayak Henry Neeman Kaylea Nelson Hai Minh Nguyen Nhat Nguyen Kurt A. O'Hearn Alexey OnufrievAlexey V. Onufriev Jim Openshaw Anita M. Orendt Michal Otyepka David A. Padua Feng Pan Sergio Pantano Ioannis Paraskevakos Dawn Paschal Ron Payne Lee G. Pedersen Lisa Perez Ha B. Pham Constantine D. Polychronopoulos Ruxi Qi Ali Rahnamoun Sanjay Ranka Ali Risheh Daniel R. Roe Adrian E. Roitberg Amit Roy Romelia Salomón-Ferrer Joel H. Saltz Patrick Schmitz Stephan Schott-Verdugo Michael L. Scott Bruce Segee Kiumars Shahrokh Akhil Shajan Julia Sheats Jana Shen Andrew H. Sherman Howard Jay Siegel Alan Sill Carlos Simmerling Christopher Simmons Shawn D. Slavin Preston M. Smith Ryan Snyder Jirí Sponer Dan C. Stefanescu Craig A. Stewart Alan Sussman Jason M. Swails Robert K.-Z. Tan Julien C. Thibault Karen A. TomkoKaren Tomko Ermal Toto Abdulnour Y. Toukmaji Le-Thuy T. Tran Thanh N. Truong Scott A. Valcourt Leslie G. Valiant Lucas Varella Ross C. Walker Bing Wang Jinan Wang Junmei Wang Haixin Wei Gil Weigand Julie Wernert Karen Wetzel Suzi White James C. Wilgenbusch Lauren Winkler Robert J. Woods Xiongwu Wu Yongxian Wu Becky Yeager Katherine A. Yelick Scott Yockel Darrin M. York Garold S. Yost Jinzhe Zeng Marie Zgarbová Shi Zhang Shiji Zhao Qiang Zhu Ralph Zottola