From: Bennion, Brian (
Date: Tue Aug 18 2015 - 14:24:08 CDT

You can do this visually quite easily.
Find the two atoms of interest.
Select the number "2" and then click on each atom. A distance for that frame will appear on the graphics window with a line between the two atoms.
Next. Click on Graphics then click on labels and then click on Bonds in the pull down menu on the left top of the window. Select the "Bond" and then click Graph.
The resulting plot can be saved in several different file formats.


You can just change the atom selections and weighting arguments in the distance.tcl script you are using.

From: [] On Behalf Of Stojanoski, Vlatko
Sent: Tuesday, August 18, 2015 10:36 AM
Subject: vmd-l: Plot of distance between two atoms vs frame number

Dear VMD users,

I'm new to VMD and my data analysis skills are limited. I'm trying to plot a distance between two atoms ( C-alpha of one residue and side chain of another) vs frame number (all frames) from a simple solvated structure simulated in NAMD. I have uploaded the .dcd in VMD and used a script that I found (distance.tcl). However, this script measures the distance between the two residue's center of the mass and not the distance between the two atoms. Any help will be greatly appreciate it. Thank you beforehand.

All the best,