Re: About calculating RMSD with rmsd.tcl

From: Peter Freddolino (
Date: Wed Oct 05 2005 - 22:22:23 CDT

how many frames do you have in your trajectory? And do you see this
change happen in the first frame, or one of the subsequent frames?

Boyang Wang wrote:

> Hi all. I am calculating the rmsd of a peptide ALA-ALA-LYS. Here is
> the .tcl file I am using:
> set outfile [open rmsd.dat w];
> set nf [molinfo top get numframes]
> set frame0 [atomselect top "resname ALA LYS" frame 0]
> set sel [atomselect top "resname ALA LYS "]
> # rmsd calculation loop
> for {set i 1 } {$i < $nf } { incr i } {
> $sel frame $i
> $sel move [measure fit $sel $frame0]
> puts $outfile "[measure rmsd $sel $frame0]"
> }
> close $outfile
> I put "resname ALA LYS" in the script because I think this is a way to
> include the whole protein. I also tried to replace the "resname ALA
> LYS" by "protein".
> Now I have a problem. After I type in "source rmsd.tcl" in the
> TKconsole interface, vmd finishes the calculation, but I have found
> that the position of the peptide has suddenly shifted a little bit
> (~0.2 Angstrom), and I see this shift in the calculated rmsd.dat. Just
> to repeat, this "shift" happens exactly when I hit "enter" after I
> typed in "source rmsd.tcl".
> I don't know what is wrong and would like to hear from you guys.
> Thanks for your time!
> Boyang
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