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Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching
École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, BCH-LCBC, CH-1015 Lausanne, Switzerland.
École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, BCH-LCBC, CH-1015 Lausanne, Switzerland.
University of Gävle, Faculty of Engineering and Sustainable Development, Department of Electrical Engineering, Mathematics and Science, Electronics. École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, BCH-LCBC, CH-1015 Lausanne, Switzerland.ORCID iD: 0000-0001-8748-3890
École Polytechnique Fédérale de Lausanne (EPFL), Institute of Chemical Sciences and Engineering, BCH-LCBC, CH-1015 Lausanne, Switzerland.
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2007 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 3, no 2, p. 628-639Article in journal (Refereed) Published
Abstract [en]

We introduce a novel procedure to parametrize biomolecular force fields. We perform finite-temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, with the fragment or moiety that has to be parametrized being included in the QM region. By applying a force-matching algorithm, we derive a force field designed in order to reproduce the steric, electrostatic, and dynamic properties of the QM subsystem. The force field determined in this manner has an accuracy that is comparable to the one of the reference QM/MM calculation, but at a greatly reduced computational cost. This allows calculating quantities that would be prohibitive within a QM/MM approach, such as thermodynamic averages involving slow motions of a protein. The method is tested on three different systems in aqueous solution:  dihydrogenphosphate, glycyl−alanine dipeptide, and a nitrosyl−dicarbonyl complex of technetium(I). Molecular dynamics simulations with the optimized force field show overall excellent performance in reproducing properties such as structures and dipole moments of the solutes as well as their solvation pattern.

Place, publisher, year, edition, pages
ACS , 2007. Vol. 3, no 2, p. 628-639
National Category
Chemical Sciences
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URN: urn:nbn:se:hig:diva-40422DOI: 10.1021/ct600284fOAI: oai:DiVA.org:hig-40422DiVA, id: diva2:1710616
Available from: 2022-11-14 Created: 2022-11-14 Last updated: 2022-11-14Bibliographically approved

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Hugosson, Håkan Wilhelm

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