A. A. Mosckovskii, I. A. Kaliman, A. V. Akimov, S. S. Konyukhov, B. L. Grigorenko, A. V. Nemukhin Realization of molecular dynamics approach with rigid fragments for simulation of chemical reactions in biomolecular systems Abstract We describe a new implementation of the molecular dynamics method targeting simulations of biomolecular systems in which chemical reactions may occur. The quantum mechanical – molecular mechanical method based on the effective fragment potential theory is used for calculations of energies and forces along trajectories. In this approach, the molecular mechanical subsystem is described by the dynamics of rigid bodies, due to peculiarities of effective fragments theory. The method has been applied for modeling proton transfer along water molecules inside the gramicidin channel.
Copyright (C) Chemistry Dept., Moscow State University, 2002 |
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