**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Mon Dec 05 2011 - 17:36:58 CST

**Next message:**Aron Broom: "Re: Calculation of distance traveled by an atom"**Previous message:**M.Raviprasad: "Calculation of distance traveled by an atom"**In reply to:**M.Raviprasad: "Calculation of distance traveled by an atom"**Next in thread:**M.Raviprasad: "RE: Calculation of distance traveled by an atom"**Reply:**M.Raviprasad: "RE: Calculation of distance traveled by an atom"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

*> To NAMD users,
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*>
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*> I calculated distance traveled by an Oxygen atom (gas molecule) in the
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*> polymeric system using DCD file. In order to make sure the calculation, I
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*> used velocity to calculate the distance (distance = Velocity*time step).
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*> Velocity was taken from the velocity DCD file. However, these two values are
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*> not matching. I believe that results should be the same (not exact but
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*> close) irrespective of the methods.
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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?
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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
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*> atom?
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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).

cheers,

axel.

*> Any suggestion is appreciated
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*>
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*> Thanks
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*>
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*> Ravi
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*>
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*>
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-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science and Technology Temple University, Philadelphia PA, USA.

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