Re: Calculation of distance traveled by an atom

From: Aron Broom (
Date: Mon Dec 05 2011 - 17:38:33 CST

1) How different are the values?

2) What are the specifics of the methods you are using to do these
calculations? As in, are you using a tcl script in VMD?

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.

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.


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 ****
> Thanks****
> Ravi ****
> ** **

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