LineShapeKin Simulation is a package available both as a source M-code to execute in MATLAB and as a compiled binaries. The source M-code enables users to modify existing models or the program output for their specific needs. However, running M-code requires a license of MATLAB 2008 with Statistics and Optimization toolboxes. The compiled binaries relieve the user from a need to have Matlab. They consist of the executable for the specific platform and a set of run-time libraries that perform MATLAB-specific functions. M-code in Matlab is executed somewhat faster than the binary but using binaries allows you to run parallel computations.
This step is required whether you intend to use M-code or binaries.
Download and unpack the LineShapeKin_Simulation_4.1.4.zip in the convenient location.
Add permission to execute to run_LineShapeKin_Simulation.sh (using chmod +x on Linux/OS X).
File index.htm is the main LineShapeKin Manual. However, you should use online manuals if possible because they are likely most up-to-date.
The LineShapeKin calls the Python programs to prepare input and output for the simulations from the folder LineShapeKin_Simulation_4.1/Python/. Add a path to this folder in your ~/.cshrc (OS X, Linux):
set path = ($path path-to-this-Python-folder-on-your-computer )
2. Test operation of the program:
On a MATLAB command line type Simulate. You should see the following output:
>> Simulate
LineShapeKin Simulation ver. 4.1.1 6/12/09.
Evgenii Kovrigin, Medical College of Wisconsin
Usage: Simulate general_setup_name model_setup_name
3. Set up a simulation run:
Create a folder for you simulation anywhere. Change your MATLAB working directory to this location. Proceed with setting up your model as described in the Tutorial section Basic features of the package and an example of the simple binding process, no coupled equilibria. U model.