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 ofsystems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popularprogram 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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