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.

---

Coarse Grained Simulations using Simbody

The demo you have just seen uses SimTKcore version 1.5 (our Simulation Toolkit), which will be released on August 11, 2008. Using a generic VTK viewer (as opposed to VMD), a similar demo program can be run using SimTKcore 1.0 (available now):

• Download SimTKcore 1.0 for your platform from the Downloads page of https://simtk.org/home/simtkcore.
  
  
• Follow the instructions and run the test programs provided with the SimTKcore 1.0 release to verify your install.
  
  
• Download SimTKExamples1_0c.zip from the Examples folder. The demo program, modified to work with the 1.0 release, is named "adenylate_mobilities.1.0.cpp" and is one of the programs in the examples directory. Compile and run this and other example programs using the instructions included.
  
  Documentation for SimTKcore 1.0 can be found in the Documents section of https://simtk.org/home/simtkcore, and installation instructions are available in the Downloads section.
  

To run the demo program with the VMD viewer, you will need to:

1. Download and install SimTKcore version 1.5, available August 11, 2008 from 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.

Note: Simbios will hold a workshop on September 25-26, 2008 to introduce programmers and modelers to the essential and advanced features of SimTKcore 1.5, the latest version of the Simbios simulation toolkit. For additional information please see Simbios.stanford.edu.

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

Note: These instructions are online at Simbios.stanford.edu/EventsOfInterest/ISMBDemos.htm