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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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