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T. Strunk, M. Wolf, M. Brieg, K. Klenin, A. Biewer, F. Tristram, M. Ernst, P. J. Kleine, N. Heilmann, I. Kondov and W. Wenzel SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems Journal of Computational Chemistry 33

Version of Record online: 10 AUG 2012 | DOI: 10.1002/jcc.23089

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Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. Here, the development of a generic, versatile simulation package is reported for stochastic simulations and its application to protein conformational change, proteinprotein association, small-molecule protein docking, and simulation of the growth of nanoscale clusters of organic molecules is demonstrated. Simulation of molecular and nanoscale systems is easy to use for standard simulations via a graphical user interface and highly parallel both via MPI and the use of graphical processors.

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