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Current issue   Ukr. J. Phys. 2016, Vol. 61, N 10, p.886-892
http://dx.doi.org/10.15407/ujpe61.10.0886    Paper

Yesylevskyy S., Berezetskaya N., Olenchuk M.

Department of Physics of Biological Systems, Institute of Physics, Nat. Acad. of Sci. of Ukraine
(46, Prosp. Nauky, Kyiv 03680, Ukraine; e-mail: yesint4@gmail.com)

Comparison of Empirical Force Fields for Bacteriochlorophyll: an Influence on Hydration and Long-Time Dynamics of Bacterial Photoreaction Centers

Section: Soft Matter
Original Author's Text: English

Abstract: The choice of an adequate empirical force field for photosynthetic cofactors is the major prerequisite of realistic molecular dynamics simulations of bacterial and plant photoreaction centers. In this work, we compare two available sets of parameters for bacteriochlorophyll in extended 200 ns simulations of photoreaction centers from Rhodobacter Sphaeroides in the membrane environment. It is shown that the most popular and widely used set of parameters produces artifacts in cofactor positions and orientations. It is also shown that the hydration of cofactors may vary, by dramatically depending on the used force field. Some recommendations for the further force field development are made.

Key words: bacterial photoreaction centers, Rhodobacter Sphaeroides, molecular dynamics, force field, cofactor hydration.