**From:** Aron Broom (*broomsday_at_gmail.com*)

**Date:** Mon Dec 05 2011 - 17:38:33 CST

**Next message:**Axel Kohlmeyer: "Re: Calculation of distance traveled by an atom"**Previous message:**Axel Kohlmeyer: "Re: 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 ]

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.

~Aron

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
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*> are 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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*>
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*> What am I doing wrong? ****
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*>
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*> Is there any other way to calculate and verify the distance travelled by
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*> an atom?****
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*>
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*> 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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*>
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