Demo README:

Input:
Sample input file, input pdb, and trajectories are given to test run md2pathMain.m
A sample residue table for the pdb is provided in the database folder. Other reference structures will be downloaded when running md2pathMain.m

Output: 
Expected output for given short trajectories is in md2path folder. Note that the provided trajectories are too short to output anything meaningful!!!
This also means that pathway calculation will fail starting from the sample trajectories, since entropies would not converge
Actual pathway calculation from full trajectories is in md2path/alloPathCalc_Example

Running simulations:
gromacs_input_files.zip contains all the needed files to run full length simulations on GPU machines
Simulations can also be run on CPU with proper changes to gpu_gromacs.sh
