Instructions for running ExampleAdenylateMobilitiesVMD

You must already have the SimTK core binaries installed from SimTK.org and compiled ExampleAdenylateMobilitiesVMD.

#  Download VMD for your platform from http://www.ks.uiuc.edu/Research/vmd/ and install.

# Locate the ThreeAdenylates.pdb and the VMD state file adenylates.vmd in this directory.

# Start VMD and load the pdb file (ThreeAdenylates.pdb) using the "File --> New Molecule" command, and then load the VMD state file (adenylates.vmd) using the "File --> Load State" command. 
You should see a static picture of three adenylatyes.

# in VMD 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

Do not hit "connect yet", but do not close the IMD connect window.

# Run adenylate_mobilitiesVMD and when prompted, go to the VMD "IMD connect" window, verify that you have the settings from the previous step and hit "connect".
 
YOU WILL SEE THE SIMULATION in VMD. 

Note: if you are running on a windows machine and have an older GPU and the animation appears sluggish select CTR-ALT-DEL to bring up the task manager.
Go to Processes and find VMD. Right click the VMD process and set the priority of VMD to "above normal".