MBN Explorer is designed for studying a broad range of physical, chemical and biological systems and materials by computing their energies, optimizing molecular structures, as well as through different types of molecular dynamics and stochastic dynamics simulations. Universality is an important feature of MBN Explorer, which allows modeling of a large number of very different molecular systems with the sizes ranging from atomic to mesoscopic and multiscale processes therein.
Library of interatomic potentials and force fields
MBN Explorer operates with a large library of interatomic potentials. A distinctive feature of the program is the possibility to combine various interatomic potentials from the library of potentials implemented in MBN Explorer and utilize them in different types of molecular dynamics, optimization or energy calculations. The potentials implemented in MBN Explorer include pairwise and many-body potentials, molecular mechanics force fields (e.g. CHARMM force field), which are widely accepted for studying bio- and nanosystems, as well as the unique ones, such as reactive CHARMM (rCHARMM) and other reactive force fields.
The file format of molecular mechanics force field used by MBN Explorer is the same as used in the programs CHARMM, XPLOR and NAMD. This compatibility allows the further extension of the applicability ranges of MBN Explorer for studies of a broad range of biological molecules. The results of MBN Explorer calculations can be visualized and analyzed by means of MBN Studio. The format of output data obtained in the course of calculations with MBN Explorer is also compatible with other standard visualization programs VMD and Chemcraft.
Apart from the standard algorithms, MBN Explorer is equipped with unique algorithmic implementations that enhance significantly the computational modeling capacities in various research and technological areas. In particular, MBN Explorer supports reactive and irradiation-driven molecular dynamics, advanced modeling of a large variety of MBN systems and stochastic processes therein by means of stochastic dynamics, simulations of MBN systems in various external fields, atomistic simulations of ultra-relativistic charged particles' propagation and channeling through oriented crystals with accounting for ionization energy losses and radiation damping, photon emission by ultra-relativistic charged particles, and many more.
By means of advanced stochastic dynamics algorithms, MBN Explorer enables simulations of MBN systems' dynamics on the time scales significantly exceeding the limits for the conventional atomistic MD. Such multiscale dynamics approach is ideal for systems in which details of their atomistic dynamics become excessive and the overall behavior of a system can be reproduced through kinetic rates for the dominating modes of motion and probabilities of the key processes occurring in the system. This important feature of MBN Explorer significantly expands its application areas and goes beyond the limits of other MD codes, usually unable to deal with multiscale modeling.
Despite the universality, the computational efficiency of MBN Explorer is comparable to or even higher than the computational efficiency of other software packages with much more limited scopes and modeling capacities, making MBN Explorer a favorable alternative with respect to such codes.
The important feature of MBN Explorer is the extensibility of the code. It is achieved through the object-oriented programming with C++. The modular design of the code allows an easy integration of new algorithms and techniques for MD simulations.