Calculation of Conformational Free Energies with the Focused Confinement Method
We introduce the focused confinement method, a reaction coordinate-free simulation approach for the calculation of conformational free energies. These are obtained in a series of restrained simulations that transform part of the molecule of interest to independent harmonic oscillators resulting in m...
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| Veröffentlicht in: | Journal of chemical theory and computation 2019-12, Vol.15 (12), p.6760-6768 |
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| container_title | Journal of chemical theory and computation |
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| creator | van der Vaart, Arjan Orndorff, Paul B Le Phan, Sang T |
| description | We introduce the focused confinement method, a reaction coordinate-free simulation approach for the calculation of conformational free energies. These are obtained in a series of restrained simulations that transform part of the molecule of interest to independent harmonic oscillators resulting in mixed harmonic–anharmonic states. It is shown that the free energy difference between these mixed states can be readily calculated through the construction of chimeric trajectories. By focusing the confinement to the conformationally active region, the method requires fewer restrained simulations than the traditional confinement method, which eases the treatment of large systems. The accuracy and efficiency of the method is demonstrated for implicitly and explicitly solvated systems. |
| doi_str_mv | 10.1021/acs.jctc.9b00590 |
| format | Article |
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Chem. Theory Comput</addtitle><description>We introduce the focused confinement method, a reaction coordinate-free simulation approach for the calculation of conformational free energies. These are obtained in a series of restrained simulations that transform part of the molecule of interest to independent harmonic oscillators resulting in mixed harmonic–anharmonic states. It is shown that the free energy difference between these mixed states can be readily calculated through the construction of chimeric trajectories. By focusing the confinement to the conformationally active region, the method requires fewer restrained simulations than the traditional confinement method, which eases the treatment of large systems. The accuracy and efficiency of the method is demonstrated for implicitly and explicitly solvated systems.</description><subject>Anharmonicity</subject><subject>Confinement</subject><subject>Free energy</subject><subject>Harmonic oscillators</subject><subject>Mathematical analysis</subject><subject>Simulation</subject><issn>1549-9618</issn><issn>1549-9626</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><recordid>eNp1kD1PwzAQhi0EoqWwMyFLLAyknO0kTkYUtYBU1AVmy3EuNFUSFzsR4t-TftABicl30vO-1j2EXDOYMuDsQRs_XZvOTNMcIErhhIxZFKZBGvP49DizZEQuvF8DCBFycU5GgsUiFZCMyTLTtelr3VW2pbakmW1L65rdrms6d4h01qL7qNDTr6pb0W6FdG5N77HY0VWLDbYdfcVuZYtLclbq2uPV4Z2Q9_nsLXsOFsunl-xxEWgRh12Qmhwlh3DYTBkXkTSRzItQyzDiCZQs5SAlJJLlZYyslJpHTJiigITnsZEgJuRu37tx9rNH36mm8gbrWrdoe6_4cB1LRcKjAb39g65t74brthSPZBgCyIGCPWWc9d5hqTauarT7VgzUVrYaZKutbHWQPURuDsV93mBxDPzaHYD7PbCL_n76b98PT1iJqg</recordid><startdate>20191210</startdate><enddate>20191210</enddate><creator>van der Vaart, Arjan</creator><creator>Orndorff, Paul B</creator><creator>Le Phan, Sang T</creator><general>American Chemical Society</general><scope>NPM</scope><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/0000-0002-8950-1850</orcidid></search><sort><creationdate>20191210</creationdate><title>Calculation of Conformational Free Energies with the Focused Confinement Method</title><author>van der Vaart, Arjan ; Orndorff, Paul B ; Le Phan, Sang T</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a364t-9cbe7204a36cf6d57c57bd4a745280f1920770871bf6e1f7a2513cdd082b6c703</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Anharmonicity</topic><topic>Confinement</topic><topic>Free energy</topic><topic>Harmonic oscillators</topic><topic>Mathematical analysis</topic><topic>Simulation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>van der Vaart, Arjan</creatorcontrib><creatorcontrib>Orndorff, Paul B</creatorcontrib><creatorcontrib>Le Phan, Sang T</creatorcontrib><collection>PubMed</collection><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>van der Vaart, Arjan</au><au>Orndorff, Paul B</au><au>Le Phan, Sang T</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Calculation of Conformational Free Energies with the Focused Confinement Method</atitle><jtitle>Journal of chemical theory and computation</jtitle><addtitle>J. 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| language | eng |
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| source | American Chemical Society |
| subjects | Anharmonicity Confinement Free energy Harmonic oscillators Mathematical analysis Simulation |
| title | Calculation of Conformational Free Energies with the Focused Confinement Method |
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