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 the molecular dynamics and random walk dynamics (kinetic Monte Carlo) simulations. Universality is an important feature of MBN Explorer, which allows modeling of large number of molecular systems and processes (e.g. atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, nanostructured materials, nanofractals, etc, composite systems like a metallic nanoparticles interacting with a biomolecule, or a DNA penetrating through a nanopore) by means of exploiting a broad variety of interatomic potentials of different kind.
Tunable force fields
MBN Explorer includes a large variety of interatomic potentials. A distinctive feature of the program is the possibility to combine various interatomic potentials from a large library of the potentials available in the package. The potentials implemented in MBN Explorer include pairwise, many-body, and molecular mechanics potentials which are widely accepted for studying bio- and nanosystems.
The file format of molecular mechanics force field used by MBN Explorer is the same as used in the CHARMM (http://www.charmm.org/), XPLOR (http://cns-online.org/v1.3/) and NAMD (http://www.ks.uiuc.edu/Research/namd/) programs. This compatibility allows one to apply MBN Explorer for calculations of a broad range of biological molecules with minimal efforts. The format of output data obtained in the course of calculations with MBN Explorer is compatible with standard visualisation programs VMD (http://www.ks.uiuc.edu/Research/vmd/) and Chemcraft (http://www.chemcraftprog.com).
Apart from many standard algorithms, MBN Explorer contains also unique algorithmic implementations which are useful in particular application areas. For instance, it allows flexible coarse graining, i.e. grouping of particles into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom in the system. This algorithm is especially useful for MD simulations of large molecular systems, having well defined interacting constituent parts, which could be treated as frozen. Note that most of other MD codes do not allow grouping of atoms in rigid bodies. Another examples include the unique algorithm for simulations of relativistic particles channeling through oriented crystals, simulation of radiation damage processes and IDMD.
MBN Explorer allows one to perform stochastic MC dynamics of molecular systems on the time scales significantly exceeding those of the conventional atomistic MD simulations. Such multiscale dynamics approach is ideal for the systems in which the details of their dynamics on the atomic scale are not so important, and can be parametrised through the kinetic rates for the dominating transformations occurring in the system. This important feature of MBN Explorer expands significantly its application areas and goes beyond the limits of other MD codes usually unable to deal with the multiscale modeling.
Despite the universality, the computational efficiency of MBN Explorer is comparable to and often even higher then the computational efficiency of other software packages, making MBN Explorer often a favorable choice.
The primary design objective for MBN Explorer is extensibility and maintainability of the code. To achieve this goal, the MBN Explorer code implements an object-oriented approach with C++. The modular design of the code allows easy integration of new algorithms and techniques for MD simulations.