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Indiana University

Summary:

Indiana University is a major multi-campus public research institution, grounded in the liberal arts and sciences, and a world leader in professional, medical, and technological education. Indiana University’s mission is to provide broad access to undergraduate, graduate, and continuing education for students throughout Indiana, the United States, and the world, as well as outstanding academic and cultural programs and student services. Indiana University seeks to create dynamic partnerships with the state and local communities in economic, social, and cultural development and to offer leadership in creative solutions for 21st century problems. Indiana University strives to achieve full diversity, and to maintain friendly, collegial, and humane environments, with a strong commitment to academic freedom.

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Software

  • Molecular Dynamics/Order Parameter eXtrapolation for Bionanosystem Simulations ( Software )

    The MD/OPX code is designed for the simulation of nanoscale systems with all-atom resolution over milliseconds or longer. The methodology makes use of the extrapolation of slowly evolving order parameters to accelerate MD. The order parameters are generated automatically from orthogonal polynomials of atomic coordinates and capture the slow behaviors of the nanostructure and the host medium in which it resides. The method has rigorous justification in the all-atom multiscale analysis of the Liouville equation for dynamical nanosystems and includes the following features: (a) averaging replica short MD runs with different atomic velocity initializations to accurately incorporate a more representative set of configurations as needed to extrapolate order parameters over long time periods (b) reconstructing the atomic-scale configuration after OPX by energy-minimizing the high energy configurations, heat, anneal and equilibrate the system to target temperature through short-time MD runs (c) automatically choosing of the critical number of order parameters needed for accurate modeling (d) achieving the simulation of bionanosystems in host media under biological conditions with periodic boundary conditions applied and (e) performing accurate all-atom dynamics simulations by tracking their output energies, temperature, pressure, etc.

    Keywords: all-atom multiscale analysis, bionanosystems, macromolecules, MD/OPX, molecular dynamics, nanosystems, order parameters, statistical mechanics, structural transitions, viruses.


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Last updated: 2013-10-01T12:53:57.163-05:00

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