  The concept of molecular mechanics force field has been widely accepted
nowadays for studying various processes in 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.
