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MesoBioNano explorer—A universal program for multiscale computer simulations of complex molecular structure and dynamics
Author(s) -
Solov'yov Ilia A.,
Yakubovich Alexander V.,
Nikolaev Pavel V.,
Volkovets Ilya,
Solov'yov Andrey V.
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23086
Subject(s) - universality (dynamical systems) , molecular dynamics , computer science , software , statistical physics , degrees of freedom (physics and chemistry) , computational science , theoretical computer science , biological system , physics , chemistry , computational chemistry , quantum mechanics , biology , programming language
Abstract We present a multipurpose computer code MesoBioNano Explorer (MBN Explorer). The package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure as well as to consider the molecular and random walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, and so on. A distinct feature of the program, which makes it significantly different from the existing codes, is its universality and applicability to the description of a broad range of problems involving different molecular systems. Most of the existing codes are developed for particular classes of molecular systems and do not permit multiscale approach while MBN Explorer goes beyond these drawbacks. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes. © 2012 Wiley Periodicals, Inc.