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8.10 Action Commands
8.10.2 atomiccorr
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.
AvgCorr(a, b) =
∑ Va (i)·Vb (i)
N
8.10.3 atomicfluct
atomicfluct [out <filename>] [<mask>] [byres | byatom | bymask] [bfactor]
[start <start>] [stop <stop>] [offset <offset>]
out <filename> Write data to file named <filename>
[<mask>] Calculate fluctuations for atoms in <mask> (all if not
specified).
byres Output the average (mass-weighted) fluctuation by residue.
bymask Output the average (mass-weighted) fluctuation for all
atoms in <mask>.
byatom (default) Output the fluctuation by atom.
[bfactor] Calculate atomic positional fluctuations squared and
weight by 83 π 2 ; this is similar but not necessarily
equivalent to the calculation of crystallographic B-factors.
[<start>] Frame to begin calculation at (default 1).
[<stop>] Frame to end calculation at (default last).
[<offset>] Frames to skip between calculations (default 1).
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