Deca-alanine example:

Step 0: building the system (a stretched deca-alanine)
cd 0-leap
make ! generate parameters, coordinates, and a pdb file
cd ..

step 1: relaxing the system
cd 1-relax
./do.sh ! relaxes the system
cd ..

step 2: compressing the system
cd 2-smd
./do.sh ! uses SMD to compress the system
./extract.sh ! picks four compressed conformation from SMD trajectory
cd ..

step 3: multple walker ABMD without selection algorithm
cd ../3-abmd
./do.sh ! runs ABMD and generates free energies every 100 ps
./analyze.sh ! progress of a particular delta F (f(34.0)-f(20.0))
cd ..

step 4: multple walker ABMD with selection algorithm
cd ../4-abmds
./do.sh
./analyze.sh
cd ..

step 5: multple walker driven ABMD
cd ../5-dabmd
./do.sh
./analyze.sh
cd ..

step 7:
./fig.sh ! generates figures using gnuplot
