Trajectory Smooth 1.1

REQUIREMENTS: VMD Version 1.7 or greater

  Computes the average position in $width frames of the atoms in the
  selection $sel and moves this sliding window through time. Let's say
  you choose a window of width 7, then the current frame, the three
  preceding ones and the three following frames are used to compute the
  average position. This results in a smoothed trajectory which will be
  saved as dcd with the name $file.

  Depending on the window size you will be able to see net movements of
  residues and get rid of some of the thermal noise.

  You can limit the averaging to specified frames using the
  'beg $firstframe' and 'end $lastframe' options. Instead of $lastframe
  you can simply type 'last' if you mean the last frame of the loaded
  dcd trajectory.
  Note that your original trajectory is transformed into the averaged
  one, you can automatically reload the original using the 'restore 1'
  Through the option 'crop 1' you can automatically crop the trajectory
  to the size specified in the beg/end statements

  The averaging procedure effects only the selection you specified, so
  might get strange atom distances at the fringes. Therefore you should
  include everything you want to look at in the selection. But careful,
  it could become quite slow then. (for rhodopsin with about 5600 atoms
  it takes about 1-2 seconds per frame on my linux box)

  sliding_avg_pos $sel $width $file [beg $firstframe] [end $lastframe]
  [restore 1/0] [crop 0/1]

  set sel [atomselect top "protein"]
  sliding_avg_pos $sel 9 slide_prot10.dcd beg 0 end 100 crop 1
  sliding_avg_pos $sel 9 slide_prot10.dcd beg 0 end last restore 1


	Jan Saam (