Di-alanine example:

Mahmoud Moradi
University of Illinois at Urbana-Champaign,
and North Carolina State University

step 0: steering the system to generate the initial pathway
(Note: for generating prmtop file and at least one initial conformation to start these simulations see B-di-alanine example!)
cd 0-smd
./job.sh ! uses ncsu_smd (steered MD) to generate 8 conformations along a linear path
cd ..

step 1: equilibrating the initial conformations (with restarint)
cd 1-pmd
./job.sh ! uses ncsu_pmd (pinned MD or restrained MD) to equilibrate the nonequilibrium conformations generated in step 0
cd ..

step 2: string method with swarms of trajectories
cd ../2-string
./job.sh ! uses ncsu_stsm (swarms-of-trajectories string method) to optimize the pathway
./analyze.sh ! extract the information from the log files
./fig.sh ! plots the results; generates string.pdf (Note: FE.txt is generated independently by ncsu_abmd and provided for plotting)
cd ..

step 3: same as step 2 with different parameters
cd ../2-string-long
./job.sh ! uses ncsu_stsm (swarms-of-trajectories string method) to optimize the pathway
./analyze.sh ! extract the information from the log files
./fig.sh ! plots the results; generates string.pdf
cd ..

In both cases (i.e., steps 2 and 3):
* Phi and Psi dihedral angles are used as collective variables
* Initial pathway is linear between (-3,3) and (1,0)
* 128 replicas are used (8 images X 16 copies)
* 100 iterations of 1 ps are performed.

In step 2, the equilibration (i.e. restrianing) is 0.98 ps/iteration and release (drifting) is 0.02 ps/iteration
In step 3, the equilibration (i.e. restrianing) is 0.9 ps/iteration and release (drifting) is 0.1 ps/iteration

Note: Free energy map (\texttt{FE.txt} file) is generated using regular ABMD (Step 3 of Example B-di-alanine).
