# atomiccorr

Calculate average correlation between motions of specified atoms.

atomiccorr [<mask>] out <filename> [cut <cutoff>] [min <min spacing>] [byatom | byres]

<mask> Atoms to calculate motion vectors for.
out <filename> File to write results to.
cut <cutoff> Only print correlations with absolute value greater than <cutoff>.
min <min spacing> Only calculate correlations for motion vectors spaced <min spacing> apart.
byatom Default; calculate atomic motion vectors.
byres Calculate motion vectors for entire residues (selected atoms in residues only).

Calculate average correlations between the motion of atoms in <mask>. For each frame, a motion vector is calculated for each selected atom from its previous position to its current position. For each pair of motion vectors Va and Vb, the average correlation between those vectors is calculated as the average of the dot product of those vectors over all N frames.

$\text{AvgCorr}(a,b) = \frac{\sum V_a (i) \cdot V_b (i)}{N}$

The value of AvgCorr can range from 1.0 (correlated) to 0.0 (no correlation) to -1.0 (anti-correlated). For example, to calculate the correlation of motion vectors between residues 1 to 13, writing to a Gnuplot-readable formatted file:

atomiccorr :1-13 out acorr.gnu byres