Calculation of distance traveled by an atom

From: M.Raviprasad (
Date: Mon Dec 05 2011 - 14:54:27 CST

To NAMD users,
I calculated distance traveled by an Oxygen atom (gas molecule) in the polymeric system using DCD file. In order to make sure the calculation, I used velocity to calculate the distance (distance = Velocity*time step). Velocity was taken from the velocity DCD file. However, these two values are not matching. I believe that results should be the same (not exact but close) irrespective of the methods.
What am I doing wrong?
Is there any other way to calculate and verify the distance travelled by an atom?
Any suggestion is appreciated



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