From: Nuno R. L. Ferreira (
Date: Thu Nov 17 2005 - 03:31:13 CST

Hi Andrea, again ;-)

About the issue of running vmd in non gui mode.
You could use the comand vmd -dispdev text -e script -args arg1 arg2
This will run the comands under vmd issued in file scripts, and we could also parse some arguments to vmd also. These ones will be stored in the list variable argv.
Check it in vmd manual (1.8.3) pgs 165-167.

About the proc, I think that you need to work with the frame comand inside the atomselections, for this to work,
like set sel [atomselect top backbone frame $nframe].

Best regards,
  ----- Original Message -----
  From: andrea spitaleri
  Sent: Thursday, November 17, 2005 8:50 AM
  Subject: vmd-l: calculate rmsd in a loop:feedback [sorry if you get it twice]

Hi all,
first this is my first script in tcl/vmd and I need of course feedback.
I have 100 structures and I want to calculate the rmsd in a such way:
structure_1 structure_2 rmsd
1 2 rmsd12
1 3 rmsd13
1 4 rmsd14
1 100 rmsd1100
2 3 rmsd23
2 4 rmsd24
and so on.
Below there is a script but it does not work properly. Could someone
help me to understand what is wrong in it. Second, to run it, do I need
to run in vmd console or can I run in a shell like vmd -script
script,without gui ?

proc calculate_rmsd {}{
for { set i 1 } { $i < 100 } { incr i } {
# pro is the root of the name of my structures
        mol load pdb pro_i.pdb
        set sel1 [atomselect "backbone"]
        for { set j i+1 } { $j < 100 } { incr j } {
                set sel2 [atomselect j "backbone"]
                set rmsd [measure rmsd $sel1 $sel2]
                puts RMSD of $i $j is $rmsd



  Andrea Spitaleri
  Dulbecco Telethon Institute
  c/o DIBIT Scientific Institute
  Biomolecular NMR, 1B4
  Via Olgettina 58
  20132 Milano (Italy)



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