RE: Calculation of distance traveled by an atom

From: M.Raviprasad (
Date: Mon Dec 05 2011 - 23:19:54 CST

From: Aron Broom []
Sent: Monday, December 05, 2011 5:39 PM
To: M.Raviprasad
Subject: Re: namd-l: Calculation of distance traveled by an atom

1) How different are the values?
difference is significant at each time steps ( 20% to 100 %)

2) What are the specifics of the methods you are using to do these calculations?
Take the coordinates from COOR.DCD file and find distance between two time frames.
Take the resulted velocities from VEL.DCD file and multiply by time step.
As in, are you using a tcl script in VMD?
It is a simple calculation So.........

There isn't a lot of information to go on here, but assuming you are doing everything correctly I'd guess at a rounding error due to many summations over a low precision variable.
No......... the difference is not from rounding error.

To address the above point, have you tried comparing the distance through both calculation methods for just a single timestep?
Since you aren't doing any summations these should be extremely close.
No. that is my worry!!!!!!!!!!!!!


On Mon, Dec 5, 2011 at 3:54 PM, M.Raviprasad <<>> wrote:
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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