Presentation-SC2001

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/)

ProtoMol (simulation)

VMD (visualization)

IMD

BioCoRE (web services)

Presentation-SC2001

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/)

Presentation-SC2001

ProtoMol

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--parallel software framework for the simulation of bio-molecules

ProtoMol is open source and available at http://www.cse.nd.edu/~lcls/Protomol.html

Presentation-SC2001

• 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/)

VMD