RE: Calculation of distance traveled by an atom

From: M.Raviprasad (
Date: Mon Dec 05 2011 - 23:11:19 CST

-----Original Message-----

From: Axel Kohlmeyer []

Sent: Monday, December 05, 2011 5:37 PM

To: M.Raviprasad


Subject: Re: namd-l: Calculation of distance traveled by an atom

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.

I understand that we cannot predict the trajectory by simply doing the calculation. But velocities stored in the VEL.DCD file were calculated based on the atomic positions stored in the coordinate DCD file. So I would expect to have approximately same distance between two time frames in both ways (Coordinate DCD and Velocity DCD).

> What am I doing wrong?

you are completely ignoring the fact how time integration works

I understand that the time integration for coordinates and velocities are different. But stored coordinates and velocities are for the same time step. So I would think that integration time would not increase the error in the approximate calculation.

and the fact that atomic velocities are significantly impacted by high frequency vibrations and librations, that would integrate out on long time scales.

But, these vibrations due to the system temperature will be adjusted by rescaling the velocities. So I do not think much of a problem with this in the calculation of distances.

> 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).

I agree that the coordinate dcd is perfect for distance calculation.





> Any suggestion is appreciated


> Thanks


> Ravi



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

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