SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems
| Autor: | Matthias Ernst, Moritz Wolf, Martin Brieg, Ivan Kondov, Nana Heilmann, Wolfgang Wenzel, P. J. Kleine, Konstantin V. Klenin, A. Biewer, Frank Tristram, Timo Strunk |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
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Molecular Protein Conformation Computer science Monte Carlo method Molecular simulation Molecular Dynamics Simulation 01 natural sciences Organic molecules Computational science 03 medical and health sciences Molecular dynamics 0103 physical sciences Nanotechnology NATURAL sciences & mathematics Simulation 030304 developmental biology Graphical user interface 0303 health sciences 010304 chemical physics business.industry Proteins General Chemistry Nanostructures Computational Mathematics ddc:500 business Monte Carlo Method Algorithms |
| Zdroj: | Journal of computational chemistry, 33 (32), 2602-2613 |
| ISSN: | 2602-2613 0192-8651 1096-987X |
| Popis: | Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation package for stochastic simulations and demonstrate its application to protein conformational change, protein–protein association, small-molecule protein docking, and simulation of the growth of nanoscale clusters of organic molecules. Simulation of molecular and nanoscale systems (SIMONA) is easy to use for standard simulations via a graphical user interface and highly parallel both via MPI and the use of graphical processors. It is also extendable to many additional simulations types. Being freely available to academic users, we hope it will enable a large community of researchers in the life- and materials-sciences to use and extend SIMONA in the future. SIMONA is available for download under http://int.kit.edu/nanosim/simona. © 2012 Wiley Periodicals, Inc. |
| Databáze: | OpenAIRE |
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