Equilibration (Part 5)

Data analysis is the most non-standard part of any molecular dynamics simulation project.  Often times, folks ended up having to write their own program to analyze the trajectory in the way they want.  But for standard processing of the trajectory, carnal and ptraj are quite competent in handling such needs.  In this section, we'll go through some of the common uses of ptraj.

1. fixing AMBER trajectory:

At this point, we have collected about 100 ps worth of MD trajectory.  You can visualize the trajectory now with the VMD program from UIUC.  But when you play the movie, you will notice that the water box becomes diffused after a while.  This can be easily fixed by re-imaging the trajectory using ptraj

Initial:

Final:

Reimaging trajectory input:

save this input and call it "ptraj.in" and then run ptraj as follows:

Basically, this will cause ptraj to read in the original trajectory file created by sander and recenter the coordinates to the center of mass of the protein and then re-image the periodic box to make it look nice and squarely.  Finally, it will calculate the rmsd of each frame using the first frame as the reference and superimposing to the C-alpha atoms exclude two residues from each terminal end.  The resulting superimposed frames are then written out to a new trajectory file called wt1mg_eq_nice.crd stripped of the box information at the end of each frame.

On the screen, you should see something like this:

The RMSD plot shown here demonstrates that the backbone conformation has reached a stationary state after about 20 ps.  We can now proceed to collecting production data.

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