From: Vermaas, Joshua (
Date: Fri Dec 15 2017 - 15:37:27 CST

Hi Rabeta,

You can do anything with a script! This will get you the distance between two atomselections, sel1 and sel2.

veclength [vecsub [measure center $sel1] [measure center $sel2]]

You can also use the colvars interface to do the same thing, although I don't have the exact syntax memorized. In terms of displaying the information, its typically easiest to just pick two representative atoms that are always near the center of their respective groups, and then using the bond label feature to track the distance visually. Its totally up to you though.

-Josh Vermaas

On 12/15/2017 02:30 PM, Rabeta Yeasmin wrote:
Dear VMD users,

I am wondering if there is any way in VMD to calculate distance between two groups of atoms.

Rabeta Yeasmin