RMSD matrix

rmsd_matrix 1.0
---------------
NAME 
 rmsd_matrix - calculates a matrix of rmsd between each given 
 frame in a trajectory
SYNOPSIS 
 rmsd_matrix -mol [top] -seltext [backbone] -frames [all] 
 -fit [backbone] -o 
DESCRIPTION
 This VMD script calculates the RMSD between every given frame in a
 trajectory and saves it to a file, which you can plot with your
 favorite program. By default, the rmsd is calculated based on the
 backbone. An initial least-squares fit of all given frames with
 respect to the first given frame is always performed, unless the
 option '-fit none' is used. By default, the initial fitting is
 based on the backbone.
 -mol 
 molid (default: top)
 
 -seltext
 an atom selection to calculate the rmsd is generated based on
 this option (default: backbone)
 
 -frames
 frames used in the analysis, following the common syntax used
 in VMD: <begin:end> or <begin:step:end> or all or now
 (default: all)
 
 -fit
 a least-squares fit is performed by default, using an atom
 selection generated based on this option (default: backbone);
 to disable the initial fitting, use -fit none
 
 -o
 output file name (if not specified, data is printed on the
 screen)
 
DOWNLOAD THE FILE:
	rmsd_matrix.tcl
AUTHOR:
	Leonardo Trabuco (ltrabuco@ks.uiuc.edu)