Di-alanine example:

Step 0: building the system (di-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: steering the system
cd 2-smd
./do.sh ! uses SMD to generate more conformations
./extract.sh ! picks two conformation from SMD trajectory
cd ..

step 3: multple iwalker ABMD without selection (2D)
cd ../3-abmd
./do.sh ! runs ABMD
./analyze.sh ! extract the free energies (FE.txt)
cd ..

step 4: multple iwalker ABMD wit selection without stopping criterion
cd ../4-abmd-S
./do.sh ! runs ABMD with the selection algorithm
./analyze.sh ! extract the free energies (FE.txt) and weights (W.txt)
cd ..

step 5: multple iwalker ABMD wit selection with stopping criterion (epsilon=0.001)
cd ../5-abmd-S-0.001
./do.sh ! runs ABMD with the selection algorithm
./analyze.sh ! extract the free energies (FE.txt) and weights (W.txt)
cd ..

step 6: multple iwalker ABMD wit selection with stopping criterion (epsilon=0.01)
cd ../6-abmd-S-0.01
./do.sh ! runs ABMD with the selection algorithm
./analyze.sh ! extract the free energies (FE.txt) and weights (W.txt)
cd ..

step 7: making figures with gnuiplot
./fig.sh
