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Interactive Molecular Dynamics (IMD)

Interactive Molecular Dynamics (IMD). IMD allows the user to guide and receive feedback from a running simulation Our demo illustrates IMD using the following components Visualization program (VMD, UIUC) Simulation program (ProtoMol, Notre Dame) IMD API (UIUC/Notre Dame)

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Interactive Molecular Dynamics (IMD)

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  1. Interactive Molecular Dynamics (IMD) • IMD allows the user to guide and receive feedback from a running simulation • Our demo illustrates IMD using the following components • Visualization program (VMD, UIUC) • Simulation program (ProtoMol, Notre Dame) • IMD API (UIUC/Notre Dame) • Haptic Device (Phantom, Sensable Technologies) • Web based collaboratory for sharing applications and data (BioCoRE, UIUC, www.ks.uiuc.edu/Research/biocore/)

  2. Interactive Simulation Interfaces OBJECTIVE: Interactive interfaces for ProtoMol • User friendly interface to setup, monitor, and steer simulations • Ability to quickly experiment with molecules and cells APPROACH: • 3-D Visualization using OpenGL • Sockets interface between ProtoMol and visualization component • Haptic Device interface • Availability over the web through a generic GUI (BioCoRE, http://www.ks.uiuc.edu/Research/biocore/)

  3. ProtoMol ProtoMol--parallel software framework for the simulation of bio-molecules • OBJECTIVE: Make ProtoMol a more scalable parallel program • Hundreds of nodes • Heterogeneous platforms • APPROACH: • Abstract parallel layer • Dynamic load balancing • Multithreading • More scalable algorithms • Future availability of ProtoMol simulations over web (thru’ BioCoRE) ProtoMol is open source and available at http://www.cse.nd.edu/~lcls/Protomol.html

  4. VMD • VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, and lipid bilayer assemblies. • VMD is available at: http://www.ks.uiuc.edu/Research/vmd • VMD is already available as an application and data sharing model for web based collaboratory research at BioCoRE (http://www.ks.uiuc.edu/Research/biocore/)

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