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  Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation

Polyak, I., Benighaus, T., Boulanger, E., & Thiel, W. (2013). Quantum mechanics/molecular mechanics dual Hamiltonian free energy perturbation. The Journal of Chemical Physics, 139, 064105/1-064105/11. doi:10.1063/1.4817402.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-A345-6 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-A346-4
Genre: Journal Article

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 Creators:
Polyak, Iakov1, Author              
Benighaus, Tobias1, 2, Author              
Boulanger, Eliot1, Author              
Thiel, Walter1, Author              
Affiliations:
1Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              
2Lanxess Deutschland GmbH, 51369 Leverkusen, Germany, ou_persistent22              

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 Abstract: The dual Hamiltonian free energy perturbation (DH-FEP) method is designed for accurate and efficient evaluation of the free energy profile of chemical reactions in quantum mechanical/molecular mechanical (QM/MM) calculations. In contrast to existing QM/MM FEP variants, the QM region is not kept frozen during sampling, but all degrees of freedom except for the reaction coordinate are sampled. In the DH-FEP scheme, the sampling is done by semiempirical QM/MM molecular dynamics (MD), while the perturbation energy differences are evaluated from high-level QM/MM single-point calculations at regular intervals, skipping a pre-defined number of MD sampling steps. After validating our method using an analytic model potential with an exactly known solution, we report a QM/MM DH-FEP study of the enzymatic reaction catalyzed by chorismate mutase. We suggest guidelines for QM/MM DH-FEP calculations and default values for the required computational parameters. In the case of chorismate mutase, we apply the DH-FEP approach in combination with a single one-dimensional reaction coordinate and with a two-dimensional collective coordinate (two individual distances), with superior results for the latter choice.

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Language(s): eng - English
 Dates: 2013-05-062013-07-182013-08-09
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1063/1.4817402
 Degree: -

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Title: The Journal of Chemical Physics
  Other : J. Chem. Phys.
Source Genre: Journal
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Publ. Info: Woodbury, N.Y. : American Institute of Physics
Pages: - Volume / Issue: 139 Sequence Number: - Start / End Page: 064105/1 - 064105/11 Identifier: ISSN: 0021-9606
CoNE: /journals/resource/954922836226