Universality
MBN Explorer is designed to study a wide range of physical, chemical and biological systems and materials by calculating their energies, optimising molecular structures and performing various types of molecular dynamics and stochastic dynamics (also sometimes referred to as random walk or kinetic Monte Carlo) simulations. Universality is an important feature of MBN Explorer, allowing the modelling of a large number of very different molecular systems ranging in size from atomic to mesoscopic and of multiscale processes therein.
Library of interatomic potentials, force fields and external fields
MBN Explorer works with a large library of interatomic potentials. A special feature of the program is the ability to combine different interatomic potentials from the library implemented in MBN Explorer and use them in different types of molecular dynamics, optimisation or energy calculations. These include: pairwise and many-body potentials, molecular mechanics force fields (e.g. CHARMM), which are widely used for the study of bio- and nanosystems, as well as unique ones, e.g. reactive CHARMM and other reactive force fields. MBN Explorer also supports simulations of the dynamics of MBN systems in the presence of external electric, magnetic, and gravitational fields, as well as electromagnetic waves.
The molecular mechanics force field file format used by MBN Explorer is the same as that used by CHARMM, XPLOR and NAMD. This compatibility allows MBN Explorer to be used to study a wide range of biological molecules. The results of MBN Explorer calculations can be visualised and analysed using MBN Studio. They are also compatible with other standard visualisation programs such as VMD and Chemcraft.
Unique algorithms
In addition to the standard algorithms, MBN Explorer is equipped with unique algorithmic implementations that significantly enhance the computational modelling capabilities in various research and technology areas. In particular, MBN Explorer supports reactive and irradiation-driven molecular dynamics, advanced modelling of a wide variety of MBN systems and stochastic processes therein by means of stochastic dynamics, simulations of MBN systems in various external fields, atomistic simulations of the propagation and channelling of ultrarelativistic charged particles through oriented crystals with consideration of ionisation energy losses and radiation damping, photon emission by ultrarelativistic charged particles and many more. The full list of algorithms implemented in MBN Explorer can be found on the dedicated webpage.
Multiscale approach
Using advanced and sometimes unique algorithms, MBN Explorer enables the simulation of MBN system dynamics on time scales far beyond the limits of conventional atomistic molecular dynamics. The methods and algorithms of multiscale theory implemented in MBN Explorer are ideal for the computational modelling of systems in which the details of their atomistic dynamics become excessive, and the overall behaviour of a system can be reproduced by kinetic rates for the dominant modes of motion and probabilities of the key processes occurring in the system. This important feature of MBN Explorer greatly expands its applications and goes beyond the limitations of other MD codes, which are typically unable to deal with multiscale modelling.
Computational efficiency
Despite its universality, the computational efficiency of MBN Explorer is comparable to, or even higher than, that of other software packages with much more limited scope and modelling capabilities, making MBN Explorer a favourable alternative to such codes. MBN Explorer supports OpenMP and MPI parallelisation.
Extensibility
The important feature of MBN Explorer is the extensibility of the code. It is achieved through object-oriented programming in C++. The modular design of the code allows easy integration of new algorithms and techniques for molecular dynamics and stochastic dynamics simulations.