Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units

Autor: Henryk Laqua, Johannes C. B. Dietschreit, Jörg Kussmann, Christian Ochsenfeld

Publikováno v: Journal of Chemical Theory and Computation. 18:6010-6020

The computationally very demanding evaluation of the 4-center-2-electron (4c2e) integrals and their respective integral derivatives typically represents the major bottleneck within hybrid Kohn-Sham density functional theory molecular dynamics simulat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b6c1ebbcb2d4bed0e6238e7433f53fa
https://doi.org/10.1021/acs.jctc.2c00509

Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition

Autor: Darren Demapan, Jörg Kussmann, Christian Ochsenfeld, Qiang Cui

Publikováno v: J Chem Theory Comput

To analyze the impact of various technical details on the results of QM/MM enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The result

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e40096223417097e90c3ab13fcfcf5bc
https://doi.org/10.1021/acs.jctc.1c00714

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

Autor: Dimitri Kosenkov, K. Birgitta Whaley, Dennis Barton, Abdulrahman Aldossary, Sam F. Manzer, Wojciech Skomorowski, Matthew Goldey, Ksenia B. Bravaya, Leif D. Jacobson, Gergely Kis, Anna I. Krylov, Aaditya Manjanath, Norm M. Tubman, Bang C. Huynh, Shane R. Yost, Barry D. Dunietz, Hainam Do, Sina Yeganeh, Shervin Fatehi, Stephen E. Mason, Warren J. Hehre, Sahil Gulania, Martin Head-Gordon, Alexander C. Paul, Jeffrey B. Neaton, István Ladjánszki, Matthias Schneider, Prashant Uday Manohar, Maximilian Scheurer, Simon A. Maurer, Adrian L. Dempwolff, Dmitry Zuev, Zachary C. Holden, Jan Wenzel, Eric J. Sundstrom, Phil Klunzinger, Jia Deng, Daniel S. Levine, Kristina D. Closser, David W. Small, Hanjie Jiang, Bernard R. Brooks, Alexandre Tkatchenko, Vale Cofer-Shabica, Xing Zhang, Nickolai Sergueev, Jonathan Thirman, Ádám Jász, Ethan Alguire, Keith V. Lawler, Chao-Ping Hsu, Saswata Dasgupta, Narbe Mardirossian, David Casanova, Pierpaolo Morgante, Andrew Behn, Vishikh Athavale, WanZhen Liang, Matthias Loipersberger, Arie Landau, Andreas Dreuw, Qingguo Feng, James R. Gayvert, Tomasz Adam Wesolowski, Thomas Kus, Alexander Zech, Daniel Lefrancois, Kirill Khistyaev, Oleg A. Vydrov, Marc P. Coons, Bushra Alam, Fenglai Liu, Alan D. Chien, Yu Zhang, Andreas W. Hauser, Stefanie A. Mewes, You Sheng Lin, Zheng Pei, Evgeny Epifanovsky, Run R. Li, Michael F. Herbst, Joseph Gomes, Thomas R. Furlani, Tim Stauch, Abel Carreras, Joonho Lee, Erum Mansoor, John M. Herbert, Yu-Chuan Su, Maxim V. Ivanov, Maximilian F. S. J. Menger, György Cserey, Ryan P. Steele, Yousung Jung, Anastasia O. Gunina, Vitaly A. Rassolov, Daniel S. Lambrecht, Zhen Tao, Fabijan Pavošević, Yves A. Bernard, Michael Diedenhofen, Igor Ying Zhang, Paul R. Horn, Hung Hsuan Lin, Roberto Peverati, William A. Goddard, Yihan Shao, Shirin Faraji, Pavel Pokhilko, Tarek Scheele, Andrew T.B. Gilbert, Triet Friedhoff, Dirk R. Rehn, Kaushik D. Nanda, Susi Lehtola, Jeng-Da Chai, Hugh G. A. Burton, Alexander A. Kunitsa, Qinghui Ge, Ádám Rák, Elliot Rossomme, Hyunjun Ji, Jing Kong, Kuan-Yu Liu, Adrian F. Morrison, Yi-Pei Li, Troy Van Voorhis, Nicholas J. Mayhall, Simon C. McKenzie, Sven Kähler, H. Lee Woodcock, Stefan Prager, Xintian Feng, Manuel Hodecker, Thomas-C. Jagau, Takashi Tsuchimochi, Peter Gill, Adrian W. Lange, Ryan M. Richard, Robert A. DiStasio, Kevin Carter-Fenk, Ying Zhu, Tim Kowalczyk, Joong Hoon Koh, Ilya Kaliman, Peter F. McLaughlin, John Parkhill, Gábor János Tornai, Caroline M. Krauter, Zhengting Gan, Eloy Ramos-Cordoba, Marcus Liebenthal, Donald G. Truhlar, Jiashu Liang, Joseph E. Subotnik, Arne Luenser, Nicole Bellonzi, Sonia Coriani, Andreas Klamt, Aleksandr V. Marenich, Shaama Mallikarjun Sharada, Zsuzsanna Koczor-Benda, Yuezhi Mao, Shannon E. Houck, Marta L. Vidal, Emil Proynov, C. William McCurdy, J. Wayne Mullinax, Mario Hernández Vera, Khadiza Begam, Alán Aspuru-Guzik, Jon Witte, Laura Koulias, Felix Plasser, Christopher J. Stein, Alec F. White, Jan-Michael Mewes, Romit Chakraborty, Ka Un Lao, Suranjan K. Paul, Teresa Head-Gordon, Karl Y Kue, Po Tung Fang, Zhi-Qiang You, Cristina E. González-Espinoza, Jie Liu, Diptarka Hait, Alan E. Rask, Phillip H.P. Harbach, Nicholas A. Besley, Kun Yao, Benjamin J. Albrecht, Benjamin Kaduk, Jae-Hoon Kim, Gergely Gidofalvi, A. Eugene DePrince, Thomas Markovich, Eric J. Berquist, Marc de Wergifosse, Alexis T. Bell, Christopher J. Cramer, Adam Rettig, Garrette Paran, Shan Ping Mao, Katherine J. Oosterbaan, Paul M. Zimmerman, Christian Ochsenfeld, J. Andersen, Magnus W. D. Hanson-Heine, Jörg Kussmann, Lyudmila V. Slipchenko, Alex J. W. Thom, Sebastian Ehlert, Atsushi Yamada, Srimukh Prasad Veccham, Kerwin Hui, Fazle Rob, Xunkun Huang, Bhaskar Rana, Sharon Hammes-Schiffer

Publikováno v: The journal of chemical physics 155(8), 084801 (2021). doi:10.1063/5.0055522
Epifanovsky, E, Gilbert, A T B, Feng, X, Lee, J, Mao, Y, Mardirossian, N, Pokhilko, P, White, A F, Coons, M P, Dempwolff, A L, Gan, Z, Hait, D, Horn, P R, Jacobson, L D, Kaliman, I, Kussmann, J, Lange, A W, Lao, K U, Levine, D S, Liu, J, McKenzie, S C, Morrison, A F, Nanda, K D, Plasser, F, Rehn, D R, Vidal, M L, You, Z-Q, Zhu, Y, Alam, B, Albrecht, B J, Aldossary, A, Alguire, E, Andersen, J H, Athavale, V, Barton, D, Begam, K, Behn, A, Bellonzi, N, Bernard, Y A, Berquist, E J, Burton, H G A, Carreras, A, Carter-Fenk, K, Chakraborty, R, Chien, A D, Closser, K D, Cofer-Shabica, V, Dasgupta, S, de Wergifosse, M, Deng, J, Diedenhofen, M, Do, H, Ehlert, S, Fang, P-T, Fatehi, S, Feng, Q, Friedhoff, T, Gayvert, J, Ge, Q, Gidofalvi, G, Goldey, M, Gomes, J, González-Espinoza, C E, Gulania, S, Gunina, A O, Hanson-Heine, M W D, Harbach, P H P, Hauser, A, Herbst, M F, Hernández Vera, M, Hodecker, M, Holden, Z C, Houck, S, Huang, X, Hui, K, Huynh, B C, Ivanov, M, Jász, Á, Ji, H, Jiang, H, Kaduk, B, Kähler, S, Khistyaev, K, Kim, J, Kis, G, Klunzinger, P, Koczor-Benda, Z, Koh, J H, Kosenkov, D, Koulias, L, Kowalczyk, T, Krauter, C M, Kue, K, Kunitsa, A, Kus, T, Ladjánszki, I, Landau, A, Lawler, K V, Lefrancois, D, Lehtola, S, Li, R R, Li, Y-P, Liang, J, Liebenthal, M, Lin, H-H, Lin, Y-S, Liu, F, Liu, K-Y, Loipersberger, M, Luenser, A, Manjanath, A, Manohar, P, Mansoor, E, Manzer, S F, Mao, S-P, Marenich, A V, Markovich, T, Mason, S, Maurer, S A, McLaughlin, P F, Menger, M F S J, Mewes, J-M, Mewes, S A, Morgante, P, Mullinax, J W, Oosterbaan, K J, Paran, G, Paul, A C, Paul, S K, Pavošević, F, Pei, Z, Prager, S, Proynov, E I, Rák, Á, Ramos-Cordoba, E, Rana, B, Rask, A E, Rettig, A, Richard, R M, Rob, F, Rossomme, E, Scheele, T, Scheurer, M, Schneider, M, Sergueev, N, Sharada, S M, Skomorowski, W, Small, D W, Stein, C J, Su, Y-C, Sundstrom, E J, Tao, Z, Thirman, J, Tornai, G J, Tsuchimochi, T, Tubman, N M, Veccham, S P, Vydrov, O, Wenzel, J, Witte, J, Yamada, A, Yao, K, Yeganeh, S, Yost, S R, Zech, A, Zhang, I Y, Zhang, X, Zhang, Y, Zuev, D, Aspuru-Guzik, A, Bell, A T, Besley, N A, Bravaya, K B, Brooks, B R, Casanova, D, Chai, J-D, Coriani, S, Cramer, C J, Cserey, G, DePrince, A E, DiStasio, R A, Dreuw, A, Dunietz, B D, Furlani, T R, Goddard, W A, Hammes-Schiffer, S, Head-Gordon, T, Hehre, W J, Hsu, C-P, Jagau, T-C, Jung, Y, Klamt, A, Kong, J, Lambrecht, D S, Liang, W, Mayhall, N J, McCurdy, C W, Neaton, J B, Ochsenfeld, C, Parkhill, J A, Peverati, R, Rassolov, V A, Shao, Y, Slipchenko, L V, Stauch, T, Steele, R P, Subotnik, J E, Thom, A J W, Tkatchenko, A, Truhlar, D G, Van Voorhis, T, Wesolowski, T A, Whaley, K B, Woodcock, H L, Zimmerman, P M, Faraji, S, Gill, P M W, Head-Gordon, M, Herbert, J M & Krylov, A I 2021, ' Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package ', Journal of Chemical Physics, vol. 155, no. 8, 084801 . https://doi.org/10.1063/5.0055522
The Journal of Chemical Physics, 155(8):084801. AMER INST PHYSICS

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange–correlation functionals, along with a suite of co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa0ad43ff193598da39e25381340f02f
https://pubmed.ncbi.nlm.nih.gov/34470363

A Fermi smearing variant of the Tamm-Dancoff approximation for nonadiabatic dynamics involving S

Autor: Laurens D M, Peters, Jörg, Kussmann, Christian, Ochsenfeld

Publikováno v: The Journal of chemical physics. 153(9)

The main shortcoming of time-dependent density functional theory (TDDFT) regarding its use for nonadiabatic molecular dynamics (NAMD) is its incapability to describe conical intersections involving the ground state. To overcome this problem, we combi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::8ea224293471b3721f29bb271886385b
https://pubmed.ncbi.nlm.nih.gov/32891109

Accelerating seminumerical Fock-exchange calculations using mixed single- and double-precision arithmethic

Autor: Christian Ochsenfeld, Henryk Laqua, Jörg Kussmann

Publikováno v: The Journal of Chemical Physics. 154:214116

We investigate the applicability of single-precision (fp32) floating point operations within our linear-scaling, seminumerical exchange method sn-LinK [Laqua et al., J. Chem. Theory Comput. 16, 1456 (2020)] and find that the vast majority of the thre

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c10b8c3d42473bfc31658a7e243b8298
https://doi.org/10.1063/5.0045084