Questions and problems?
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
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