From: Axel Kohlmeyer (
Date: Thu Sep 20 2007 - 10:20:08 CDT

On Thu, 20 Sep 2007, INPE (Ingrid Viveka Pettersson) wrote:

IP> Dear All,

dear ingrid,
IP> I am a very new VMD user and I would appreciate any help. I have
IP> run a simulation and I would like to analyse distances between
IP> different selected atoms in a serie of different frames in the
IP> trajectory. I would like to have the output as a text file so that I
IP> can use any software to get a plot. I apologize if I have missed
IP> the information in the manual.

well, the manual gives only a minimal description of what you can do.
it may be more useful to go through some of the available scripting
tutorials and have a look at the script library. also having a look
into a tcl tutorial should be helpful to get the basics of file i/o.
( try: )

the kind of analysis you want to do is very straightforward to do,
the following (untested!!) script fragments should help:

# read files and gather info
set mol [mol new "system.psf" type psf waitfor all]
mol addfile "traj.dcd" type dcd waitfor all
set nf [molinfo $mol get numframes]

# define selections for atom pairs to watch
set dist1 [atomselect $mol {index 15 45}]
set dist2 [atomselect $mol {index 23 24}]

# loop over frames and write data
set fp [open "output-dist.dat" w]

for {set i 0} {$i < $nf} {incr i} {

  $dist1 frame $i
  set d1 [$dist1 get {x y z}]
  $dist2 frame $i
  set d2 [$dist2 get {x y z}]

  puts $fp "$i [vecdist [lindex $d1 0] [lindex $d1 1]] [vecdist [lindex $d2 0] [lindex $d2 1]]"

close $fp


IP> Yours sincerely,
IP> Ingrid Pettersson
IP> ___________________________________
IP> Ingrid Pettersson
IP> Research Scientist
IP> Structure & Biophysical Chemistry
IP> Novo Nordisk A/S
IP> Novo Nordisk Park
IP> DK-2760 Måløv
IP> Denmark
IP> +45 4443 4506 (direct)
IP> +45 30754506 (mobile)
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Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.