(Note: These tutorials are meant to provide
illustrative examples of how to use the AMBER software suite to carry out
simulations that can be run on a simple workstation in a reasonable period of
time. They do not necessarily provide the optimal choice of parameters or
methods for the particular application area.)
Copyright Dwight McGee, Hailey Bureau, Caley Allen, Rigoberto Hernandez
Section 3: Analysis of Results
Now that the ASMD simulations are complete, we need to restitch the PMF output from each stage created by ASMD.py to obtain the actual PMF for each of the simulations at different velocities.
Restitch the PMF
Lets first begin with the 100 Å/ns simulations. To do this we can use the python script create.PMF.py. To get a full a list of all the available options use the -h or --help flags. In order for the script to work, all input files being stitchd must have the following naming convention jar.stage#.dat where # is the number of the stage.
Type the following command: to produce the output file jar.PMF.100ang.25tps.dat
| >create.PMF.py -s 5 -o jar.100ang.25tps.dat |
Next, create the PMF for the 10 Å/ns simulation to produce the output file jar.PMF.10ang.25tps.dat
| >create.PMF.py -s 5 -o jar.10ang.25tps.dat |
Plotting the PMF
You can use your favorite program to plot the PMFs.
For example, if you were to use the GNU graphing suite, you can type the following from the terminal command line: gnuplotgnuplot> plot "jar.PMF.100ang.25tps.dat" w l ti "100 Å/ns" lw 3 lc rgb "black", "jar.PMF.10ang.25tps.dat" w l ti "10 Å/ns" lw 3 lc rgb "blue"
As expected, the PMF for the faster velocity is higher than the slower velocity pull at the end of the pull. At faster velocities, the system has less time to adjust to the pertubation being applied, thus resulting in a higher PMF.
Things to consider: What would happen if you: employed a different solvent model, added more trajectories, pulled at a slower velocity, increased or decreased the number of stages, or pulled for a longer distance?