From: Prof. Eddie (
Date: Tue Aug 18 2015 - 15:26:01 CDT

Hi Vlatko,
You can use the graphical interface to get your first measures if you don't
need a script. Use the labels in the Mouse menu and select bond then click
on the two atoms you want. Afterwards you can see the results using
Graphics -> labels.
More details about this are here:

On Tue, Aug 18, 2015 at 12:35 PM, Stojanoski, Vlatko <>

> 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,
> Vlatko

Edward Ackad, Ph.D <>
Assistant Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390