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  On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations

Meier, K., Thiel, W., & van Gunsteren, W. F. (2012). On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations. Journal of Computational Chemistry, 33(4), 363-378. doi:10.1002/jcc.21962.

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 Creators:
Meier, Katharina1, Author
Thiel, Walter2, Author           
van Gunsteren, Wilfred F.1, Author
Affiliations:
1Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, ou_persistent22              
2Research Department Thiel, Max-Planck-Institut für Kohlenforschung, Max Planck Society, ou_1445590              

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Free keywords: QM/MM; molecular dynamics; force field; OM3; boundary conditions; BLUF
 Abstract: During the past years, the use of combined quantum–classical, QM/MM, methods for the study of complex biomolecular processes, such as enzymatic reactions and photocycles, has increased considerably. The quality of the results obtained from QM/MM calculations is largely dependent on five aspects to be considered when setting up a molecular model: the QM Hamiltonian, the MM Hamiltonian or force field, the boundary and coupling between the QM and MM regions, the size of the QM region and the boundary condition for the MM region. In this study, we systematically investigate the influence of a variation of the molecular mechanics force field and the size of the QM region in QM/MM MD simulations on properties of the photoactive part of the blue light photoreceptor protein AppA. For comparison, we additionally performed classical MD simulations and studied the effect of a variation of the type of spatial boundary condition. The classical boundary conditions and the force field used in a QM/MM MD simulation are shown to have non-neglegible effects upon the structural and energetic properties of the protein which makes it advisable to minimize computational artifacts in QM/MM MD simulations by application of periodic boundary conditions and a thermodynamically calibrated force field. A comparison of the structural and energetic properties of MD simulations starting from two alternative, different X-ray structures for the blue light utilizing flavin protein in its dark state indicates a slight preference of the two force fields used for the so-called Anderson structure over the Jung structure. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

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 Dates: 2012-02-05
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1002/jcc.21962
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Title: Journal of Computational Chemistry
Source Genre: Journal
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Publ. Info: New York : Wiley.
Pages: - Volume / Issue: 33 (4) Sequence Number: - Start / End Page: 363 - 378 Identifier: ISSN: 0192-8651
CoNE: https://pure.mpg.de/cone/journals/resource/954925489848
DOI: 10.1002/jcc.21962