Modeling MesoBioNano systems with MBN Studio made easy

Gennady B.Sushko, Ilia A.Solov'yov, Andrey V.Solov'yov
Journal of Molecular Graphics and Modelling
88
247-260
2019
abstract
This paper introduces MesoBioNano (MBN) Studio – a graphical user interfacefor a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization molecular dynamics, and kinetic Monte Carlo simulations. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner. Employing this plug-in, one can easily construct molecular systems of different geometries (e.g., spherical or ellipsoidal nanoparticles, cubic crystalline samples) with various atomic composition. The paper presents the first public release of MBN Studio and provides an overview of its significant capabilities as well as the reference point for further extensions.