Molecular Dynamics API Accelerated via GPUs

The demo you have just seen showed the significant speed up of molecular dynamics calculations using a GPU as compared to a CPU.

The Molecular Dynamics API will be released on September 1, 2008 at http://simtk.org/home/openmm. You will be able to download the reference code, as well as a version of Gromacs that uses this API and performs traditional CPU computations.

A Gromacs code using this API and running on GPUs will be released December 1, 2008.

If you are interested in early access to the code, contact Dr. Vijay Pande at pande@stanford.edu.

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Coarse Grained Simulations using Simbody

The demo you have just seen uses SimTKcore version 1.5 (our Simulation Toolkit), which was released on August 11, 2008.
To run the demo program you will need to:

1. Download and install SimTKcore version 1.5 for your platform, available from the download section of https://simtk.org/home/simtkcore, and follow the instructions for that release.
   
   
2. Download and install VMD from http://www.ks.uiuc.edu/Research/vmd/
   
   
3. Go to the Downloads section of https://simtk.org/home/tri-adenylate-demo, and download the pdb file ThreeAdenylates.pdb and the VMD state file adenylates.4.vmd. Start VMD and load the pdb file using the "File --> New Molecule" command, and then load the VMD state file using the "File --> Load State" command.
   
   
4. After you have successfully installed SimTKcore 1.5, compile adenylate_mobilities.cpp and run. When prompted, go to VMD and select "Extensions --> Simulations --> IMD connect."
   Set:
   
   a) hostname to localhost
   b) Port to 3000
   c) Timestep transfer rate to 1
   d) Timestep keep rate to 1
   
   YOU WILL SEE THE SIMULATION in VMD.

Notes:
1) Following the SimTK 1.5 release on August 11, 2008, Simbios is holding a two day workshop on September 25-26 to introduce programmers and modelers to the essential and advanced features of the toolkit. For additional information please see Simbios.stanford.edu.

2) A larger set of example programs, including the above demo program will be made available shortly in the download section of simtk.org/home/simtkcore in preparation for the SimTK 1.5 Workshop.

For general questions please contact the Simbios Director of Dissemination, Dr. Joy Ku, at joyku@stanford.edu.

Note: These instructions are online at http://simbios.stanford.edu/EventsOfInterest/Demos.htm