From: Stojanoski, Vlatko (
Date: Tue Aug 18 2015 - 12:35:48 CDT

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,