The collection of python and bash scripts to prepare and analyzing data for Molecular Dynamics simualtions. The tools are written by Kun Huang during his Ph.D for Physics under the supervision of Dr. Garcia . Everyone is welcome to use and distribute them :).

Since the tools are written in python and bash, it should work in any linux distribution. The tools are organized in following folders:

/root
	/common  
		a collection of tools for general purposes such as command-line parser.  
	/x-form   
		a collection of tools to calculate membrane density profile, x-ray form factors.  
	/membraneBuilder  
		a collection of tools to build membrane bilayers, including mixed bilayers.  
	/statAnalyze 
		a collection of tools to perform statistical analysis on dataset. 

For python scripts, please include the /root folder in PYTHONPATH evironment variable for the scripts to work. Also additional library are needed for certain tools to work, such as:

• xdr library. A C and Python library to read xdr files generated by Gromacs. The library can be downloaded from [GROMACS website] (http://www.gromacs.org/Downloads)
• numpy. A numerical library for python.