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 two conformation from SMD trajectory
cd ..

step 3: multple walker ABMD without selection (5 A resolution)
cd ../3-abmd-5A-4w
./do.sh ! runs ABMD
./analyze.sh ! extract the free energies (FE.txt)
cd ..

step 4: multple walker ABMD with selection (5 A resolution)
cd ../4-abmd-5A-4w-S
./do.sh ! runs ABMD
./analyze.sh ! extract the free energies (FE.txt) and weights (W.txt)
cd ..

step 5: multple walker ABMD without selection (1 A resolution)
cd ../5-abmd-1A-8w
cd 00
./do.sh ! runs ABMD (200 ps)
./analyze.sh ! extract the free energies (FE.txt)
cd ..
! repeat for 01 to 06 (each runs for another 200 ps)
cd ..

step 6: multple walker ABMD with selection (1 A resolution)
cd ../6-abmd-1A-8w-S
cd 00
./do.sh ! runs ABMD (200 ps)
./analyze.sh ! extract the free energies (FE.txt) and weights (W.txt)
cd ..
! repeat for 01 to 06 (each runs for another 200 ps)
cd ..

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