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
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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