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SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems.

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Title: SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems.
Authors: Strunk, T.1, Wolf, M.1, Brieg, M.2, Klenin, K.2, Biewer, A.1, Tristram, F.1, Ernst, M.1, Kleine, P. J.1, Heilmann, N.1, Kondov, I.2, Wenzel, W.1
Source: Journal of Computational Chemistry. Dec2012, Vol. 33 Issue 32, p2602-2613. 12p. 6 Diagrams, 2 Charts, 4 Graphs.
Subjects: Stochastic processes, Simulation methods & models, Protein folding, Monte Carlo method, Graphical user interfaces, Computational chemistry
Abstract: 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. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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  Data: SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems.
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  Data: <searchLink fieldCode="AR" term="%22Strunk%2C+T%2E%22">Strunk, T.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Wolf%2C+M%2E%22">Wolf, M.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Brieg%2C+M%2E%22">Brieg, M.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Klenin%2C+K%2E%22">Klenin, K.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Biewer%2C+A%2E%22">Biewer, A.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Tristram%2C+F%2E%22">Tristram, F.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Ernst%2C+M%2E%22">Ernst, M.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Kleine%2C+P%2E+J%2E%22">Kleine, P. J.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Heilmann%2C+N%2E%22">Heilmann, N.</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Kondov%2C+I%2E%22">Kondov, I.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Wenzel%2C+W%2E%22">Wenzel, W.</searchLink><relatesTo>1</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. Dec2012, Vol. 33 Issue 32, p2602-2613. 12p. 6 Diagrams, 2 Charts, 4 Graphs.
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  Data: <searchLink fieldCode="DE" term="%22Stochastic+processes%22">Stochastic processes</searchLink><br /><searchLink fieldCode="DE" term="%22Simulation+methods+%26+models%22">Simulation methods & models</searchLink><br /><searchLink fieldCode="DE" term="%22Protein+folding%22">Protein folding</searchLink><br /><searchLink fieldCode="DE" term="%22Monte+Carlo+method%22">Monte Carlo method</searchLink><br /><searchLink fieldCode="DE" term="%22Graphical+user+interfaces%22">Graphical user interfaces</searchLink><br /><searchLink fieldCode="DE" term="%22Computational+chemistry%22">Computational chemistry</searchLink>
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  Data: 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. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – SubjectFull: Protein folding
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              Text: Dec2012
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