# Process the trajectory in the top molecule, and store the distance 
# moved by each particle relative to the previous frame in the user field

# Justin Gullingsrud
# justinrocks@gmail.com
# 21 August 2005

proc colorBySpeed { } {
  set n [molinfo top get numframes]
  set all [atomselect top all]
  set oldx [$all get x]
  set oldy [$all get y]
  set oldz [$all get z]
  for { set i 1 } { $i < $n } { incr i } {
    $all frame $i
    set x [$all get x]
    set y [$all get y]
    set z [$all get z]
    set delta [list]
    foreach dx [vecsub $x $oldx] dy [vecsub $y $oldy] dz [vecsub $z $oldz] {
      lappend delta [expr {sqrt($dx*$dx + $dy*$dy + $dz*$dz)}]
    }
    $all set user $delta
    set oldx $x
    set oldy $y
    set oldz $z
  }
}