On leave from Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, Illinois 61801.
MesoBioNano explorer—A universal program for multiscale computer simulations of complex molecular structure and dynamics
Article first published online: 11 SEP 2012
Copyright © 2012 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 33, Issue 30, pages 2412–2439, 15 November 2012
How to Cite
Solov'yov, I. A., Yakubovich, A. V., Nikolaev, P. V., Volkovets, I. and Solov'yov, A. V. (2012), MesoBioNano explorer—A universal program for multiscale computer simulations of complex molecular structure and dynamics. J. Comput. Chem., 33: 2412–2439. doi: 10.1002/jcc.23086
- Issue published online: 13 OCT 2012
- Article first published online: 11 SEP 2012
- Manuscript Accepted: 5 JUL 2012
- Manuscript Revised: 30 JUN 2012
- Manuscript Received: 9 APR 2012
- Stiftung Polytechnische Gesellschaft Frankfurt am Main (A.Y.) I.S. acknowledges support as a Beckman Fellow
- nanostructures simulation;
- biomolecular simulation;
- molecular dynamics;
- structure optimization;
- multiscale approach
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.