Questions and problems?

Analysis questions

How to do energy analysis along a trajectory?
I used carnal for averaging of coordinates and obtained average interatomic diatances on a viewer. I also performed interatomic distance analysis using DIST in DECLARE. The values from the two methods were not the same. They were different in the order of 0.1 Angstromes. Why are they so different?

Consider for example a methyl group which is rotating during dynamics. If you average the coordinates, you will notice that the C-H bond distances shrink, although all in each frame the distance is ~1A. Looking at a planar analog:

                X      (Z)      X'
                 \             /
                  \           /
                   \         /
                    \       /
                     \     /
                      \   /
                       \ /

If atom X is observed at positions X and X', the average position is Z, and we can see that
      ( d(A-X) + d(A-Y) ) / 2    != d(A-Z)
The measurement of an average structure from a trajectory is not equivalent to the average of the same measurement on each set in the trajectory.
How to analyse water in an MD trajectory. I'm interested in being able to quantify the most frequently occupied water positions, and in particular the frequency of water mediated hydrogen bonds.

Long answer by Thomas Cheatham