From: Myunggi Yi (
Date: Wed May 02 2007 - 16:34:04 CDT

Dear VMD users,

I'm using vmd 1.8.5.
The following is my rmsd calculation script.
I always get a big rmsd value at some point.
Obviously this comes from "bad fitting" (checked by visulizing the trajectory)

The same result were reprodued by rmsd tool built in the GUI.
So, I opened Tkconsole, and typed the command manually at the frame.
Even with a big rmsd value, I couldn't superimposed the frame.

Is this known problem?
I attached the xmgrace file generated by VMD (rmsd tool).

proc rms { sel step file } {
    set fout [open $file w]
        set mid [$sel molid]
    set nf [molinfo $mid get numframes]
    set ref [atomselect $mid "[$sel text]" frame 0]
    set all [atomselect $mid all]
        puts $fout "0 0"
    # rmsd calculation loop
    for { set i 1 } { $i < $nf } { incr i } {
                molinfo $mid set frame $i
        $sel frame $i
        $all frame $i
        $all move [measure fit $sel $ref]
        puts $fout "[expr $i * $step] [measure rmsd $sel $ref]"
    close $fout

Best wishes,
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306
Office: (850) 645-1334

  • application/octet-stream attachment: rms.agr