Re: Calculation of distance traveled by an atom

From: Axel Kohlmeyer (
Date: Mon Dec 05 2011 - 17:36:58 CST

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.

i disagree. if it was possible to even approximately predict
the trajectory of atoms this way, we wouldn't have these
issues with requiring so much computer time to do MD
simulations of big systems.

> What am I doing wrong?

you are completely ignoring the fact how time integration works
and the fact that atomic velocities are significantly impacted
by high frequency vibrations and librations, that would integrate
out on long time scales.

> Is there any other way to calculate and verify the distance travelled by an
> atom?

i don't see why you need to "verify" the coordinate data.
the coordinate dcd file is the perfect(!) record of how each
atom has traveled during your simulation and the distance
between any two reference points is as accurate as it gets
(outside of quantum effects that don't show up in classical
MD in the first place).


> Any suggestion is appreciated
> Thanks
> Ravi

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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