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)