monitor a distance between two molecules

From: me00109_at_cc.uoi.gr
Date: Sat Aug 30 2008 - 18:06:11 CDT

Hello namd users,
Iam new in namd and Iam trying to find a way to extract information, actually
the distance between the center of the masses of two solvated molecules that I
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 a
function of time during the simulation?
I want to have a lot of values in order to plot them against time but I do not
know how to do this even for a spesific picosec.

Does anybody know?
Thank you
George

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