Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

Gennady B. Sushko, Ilia A. Solov'yov, Alexey V. Verkhovtsev, Sergey N. Volkov, Andrey V. Solov'yov
European Physical Journal D
The concept of molecular mechanics force field has been widely accepted nowadays for studying various processesin biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of
systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular
program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is
necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes
where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in
transformation and fragmentation processes involving biomolecular systems.

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