Re: Calculation of distance traveled by an atom

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 05 2011 - 23:22:53 CST

On Tue, Dec 6, 2011 at 12:11 AM, M.Raviprasad <M.Raviprasad_at_my.ndsu.edu>wrote:

> -----Original Message-----****
>
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com] ****
>
> Sent: Monday, December 05, 2011 5:37 PM****
>
> To: M.Raviprasad****
>
> Cc: namd-l_at_ks.uiuc.edu****
>
> Subject: Re: namd-l: Calculation of distance traveled by an atom****
>
> ** **
>
> On Mon, Dec 5, 2011 at 3:54 PM, M.Raviprasad <M.Raviprasad_at_my.ndsu.edu>
> 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
>
no, they are not! the *forces* are computed from the coordinates.
velocities are computed from previous velocities and the force.
please look up newton's laws.

> would expect to have approximately same distance between two time frames
> in both ways (Coordinate DCD and Velocity DCD).
>
this is nonsense.

> ****
>
> ** **
>
> > 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.
>
sorry, your reasoning would _only_ work, if there were *no* forces
at all acting between the atoms. again, see newton's laws.
we are talking *elementary* classical mechanics stuff here.

> 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.
>
huh? this statement makes even less sense than the previous ones.

> > 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.
>
so why do you need to "verify" it?

axel.

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

-- 
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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