| Affiliation: | (1) Institute of Physical Biology, University of South Bohemia, Zamek 136, 37333 Nove Hrady, Czech Republic;(2) Institute of Landscape Ecology, Academy of Sciences of the Czech Republic, Zamek 136, 37333 Nove Hrady, Czech Republic;(3) Institute of Plant Molecular Biology, Academy of Sciences of the Czech Republic, Branisovska 31, 370 05 Ceske Budejovice, Czech Republic |
| Abstract: | We developed new parameters for molecular dynamics (MD) simulations, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of chlorophyll a (Chl) and plastoquinone (PQ), and both reduced and neutral form of primary acceptor (PHO) molecule. These parameters are essential for MD simulations that can interpret various structure functional relationships during primary processes of charge separation and stabilization in photosystem 2 reaction centres. |
