RE: monitor a distance between two molecules

From: JC Gumbart (
Date: Sun Aug 31 2008 - 23:31:17 CDT

The best way to do this is using VMD (

After loading your trajectory, you can label a bond between them and then
see under Labels->Bonds the distance between them over time. Alternatively,
you can use a little tcl scripting to have more control over what you

You can find more specifics in the manual of course, and also the tutorials,
including getting started with tcl:

-----Original Message-----
From: [] On Behalf
Sent: Saturday, August 30, 2008 6:06 PM
To: NAMD list
Subject: namd-l: monitor a distance between two molecules

Hello namd users,
Iam new in namd and Iam trying to find a way to extract information,
the distance between the center of the masses of two solvated molecules that
have simulated with an MD calculation.

I have the dcd file and every other file of the simulation but how do I
calculate the distance between the two molecules, moreover the distance as
function of time during the simulation?
I want to have a lot of values in order to plot them against time but I do
know how to do this even for a spesific picosec.

Does anybody know?
Thank you

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