Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units
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 simulations. Building upon our previous works on seminume...
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description | 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 simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardwareespecially when combined with graphics processing unit accelerationimproving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine–thymine and guanine–cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems. |
doi_str_mv | 10.1021/acs.jctc.2c00509 |
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B. ; Kussmann, Jörg ; Ochsenfeld, Christian</creator><creatorcontrib>Laqua, Henryk ; Dietschreit, Johannes C. B. ; Kussmann, Jörg ; Ochsenfeld, Christian</creatorcontrib><description>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 simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardwareespecially when combined with graphics processing unit accelerationimproving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine–thymine and guanine–cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems.</description><identifier>ISSN: 1549-9618</identifier><identifier>EISSN: 1549-9626</identifier><identifier>DOI: 10.1021/acs.jctc.2c00509</identifier><language>eng</language><publisher>Washington: American Chemical Society</publisher><subject>Adenine ; Approximation ; Bonding strength ; Density functional theory ; Dynamic structural analysis ; Electronic structure ; Evaluation ; Graphics processing units ; Hydrogen bonds ; Mathematical analysis ; Molecular dynamics ; Quantum Electronic Structure ; Self consistent fields ; Simulation ; Thymine</subject><ispartof>Journal of chemical theory and computation, 2022-10, Vol.18 (10), p.6010-6020</ispartof><rights>2022 The Authors. 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B.</creatorcontrib><creatorcontrib>Kussmann, Jörg</creatorcontrib><creatorcontrib>Ochsenfeld, Christian</creatorcontrib><title>Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units</title><title>Journal of chemical theory and computation</title><addtitle>J. Chem. Theory Comput</addtitle><description>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 simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardwareespecially when combined with graphics processing unit accelerationimproving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine–thymine and guanine–cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems.</description><subject>Adenine</subject><subject>Approximation</subject><subject>Bonding strength</subject><subject>Density functional theory</subject><subject>Dynamic structural analysis</subject><subject>Electronic structure</subject><subject>Evaluation</subject><subject>Graphics processing units</subject><subject>Hydrogen bonds</subject><subject>Mathematical analysis</subject><subject>Molecular dynamics</subject><subject>Quantum Electronic Structure</subject><subject>Self consistent fields</subject><subject>Simulation</subject><subject>Thymine</subject><issn>1549-9618</issn><issn>1549-9626</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp1kclOwzAQhiMEEuudoyUuHEjxErfNsWKtBAKxnCPHHlNXiV1sRyKvxRPi0MIBiZNHnm_mn5k_y44JHhFMybmQYbSUUY6oxJjjcivbI7wo83JMx9u_MZnuZvshLDFmrKBsL_ucSQkNeBGNfUO3fe2NQpdgg4k9uu6sjMZZ0aCXBTjfo3vXgOwa4dFlb0VrZEDPpk0fAxZQ3aNnaI3tWvBGprK5jfDmv7Nn6AmCa7ohzp3O4wLyuQIbB6XZauXdh2k3pLAK3XixWgwCj95JCGGY79WaGA6zHS2aAEeb9yB7vb56ubjN7x5u5hezu1zQCYl5rYUSQKdEK6aVwpxCMZ1gwgivCeW0nrJJAgilTHMGVHNFMSs1LnlBKVHsIDtd902jvXcQYtWakI7VCAuuC1VSGZcFw2WZ0JM_6NJ1Pt1toGjBCMGcJQqvKeldCB50tfJpZd9XBFeDiVUysRpMrDYmppKzdcl35qfnv_gXv-GkQg</recordid><startdate>20221011</startdate><enddate>20221011</enddate><creator>Laqua, Henryk</creator><creator>Dietschreit, Johannes C. B.</creator><creator>Kussmann, Jörg</creator><creator>Ochsenfeld, Christian</creator><general>American Chemical Society</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7SC</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4724-8551</orcidid><orcidid>https://orcid.org/0000-0002-4189-6558</orcidid><orcidid>https://orcid.org/0000-0002-5840-0002</orcidid></search><sort><creationdate>20221011</creationdate><title>Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units</title><author>Laqua, Henryk ; Dietschreit, Johannes C. B. ; Kussmann, Jörg ; Ochsenfeld, Christian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a271t-bfadae281fd3fdd052e48701315b1252b837dae1223f53e2f5d2039f0954221d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Adenine</topic><topic>Approximation</topic><topic>Bonding strength</topic><topic>Density functional theory</topic><topic>Dynamic structural analysis</topic><topic>Electronic structure</topic><topic>Evaluation</topic><topic>Graphics processing units</topic><topic>Hydrogen bonds</topic><topic>Mathematical analysis</topic><topic>Molecular dynamics</topic><topic>Quantum Electronic Structure</topic><topic>Self consistent fields</topic><topic>Simulation</topic><topic>Thymine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Laqua, Henryk</creatorcontrib><creatorcontrib>Dietschreit, Johannes C. B.</creatorcontrib><creatorcontrib>Kussmann, Jörg</creatorcontrib><creatorcontrib>Ochsenfeld, Christian</creatorcontrib><collection>CrossRef</collection><collection>Computer and Information Systems Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of chemical theory and computation</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Laqua, Henryk</au><au>Dietschreit, Johannes C. B.</au><au>Kussmann, Jörg</au><au>Ochsenfeld, Christian</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units</atitle><jtitle>Journal of chemical theory and computation</jtitle><addtitle>J. Chem. Theory Comput</addtitle><date>2022-10-11</date><risdate>2022</risdate><volume>18</volume><issue>10</issue><spage>6010</spage><epage>6020</epage><pages>6010-6020</pages><issn>1549-9618</issn><eissn>1549-9626</eissn><abstract>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 simulations. Building upon our previous works on seminumerical exact-exchange (sn-LinK) [Laqua, H., Thompsons, T. H., Kussmann, J., Ochsenfeld, C., J. Chem. Theory Comput. 2020, 16, 1465] and resolution-of-the-identity Coulomb (RI-J) [Kussmann, J., Laqua, H., Ochsenfeld, C., J. Chem. Theory Comput. 2021, 17, 1512], the expensive 4c2e integral evaluation can be avoided entirely, resulting in a highly efficient electronic structure theory method, allowing for fast ab initio molecular dynamics (AIMD) simulations even with large basis sets. Moreover, we propose to combine the final self-consistent field (SCF) step with the subsequent nuclear forces evaluation, providing the forces at virtually no additional cost after a converged SCF calculation, reducing the total runtime of an AIMD simulation by about another 25%. In addition, multiple independent MD trajectories can be computed concurrently on a single node, leading to a greatly increased utilization of the available hardwareespecially when combined with graphics processing unit accelerationimproving the overall throughput by up to another 5 times in this way. With all of those optimizations combined, our proposed method provides nearly 3 orders of magnitude faster execution times than traditional 4c2e integral-based methods. To demonstrate the practical utility of the approach, quantum-mechanical/molecular-mechanical dynamics simulations on double-stranded DNA were performed, investigating the relative hydrogen bond strength between adenine–thymine and guanine–cytosine base pairs. In addition, this illustrative application also contains a general accuracy assessment of the introduced approximations (integration grids, resolution-of-the-identity) within AIMD simulations, serving as a protocol on how to apply these new methods to practical problems.</abstract><cop>Washington</cop><pub>American Chemical Society</pub><doi>10.1021/acs.jctc.2c00509</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-4724-8551</orcidid><orcidid>https://orcid.org/0000-0002-4189-6558</orcidid><orcidid>https://orcid.org/0000-0002-5840-0002</orcidid></addata></record> |
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subjects | Adenine Approximation Bonding strength Density functional theory Dynamic structural analysis Electronic structure Evaluation Graphics processing units Hydrogen bonds Mathematical analysis Molecular dynamics Quantum Electronic Structure Self consistent fields Simulation Thymine |
title | Accelerating Hybrid Density Functional Theory Molecular Dynamics Simulations by Seminumerical Integration, Resolution-of-the-Identity Approximation, and Graphics Processing Units |
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