title: SIMONA 1.0: an efficient and versatile framework for stochastic simulations of molecular and nanoscale systems.
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.
authors.affiliation: Institute of Nanotechnology, Karlsruhe Institute of Technology, PO Box 3640, 76021 Karlsruhe, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Strunk
authors.forename: M
authors.initials: M
authors.lastname: Wolf
authors.forename: M
authors.initials: M
authors.lastname: Brieg
authors.forename: K
authors.initials: K
authors.lastname: Klenin
authors.forename: A
authors.initials: A
authors.lastname: Biewer
authors.forename: F
authors.initials: F
authors.lastname: Tristram
authors.forename: M
authors.initials: M
authors.lastname: Ernst
authors.forename: P J
authors.initials: PJ
authors.lastname: Kleine
authors.forename: N
authors.initials: N
authors.lastname: Heilmann
authors.forename: I
authors.initials: I
authors.lastname: Kondov
authors.forename: W
authors.initials: W
authors.lastname: Wenzel
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins