# Re: Calculating displacement in a system with periodic boundary

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Tue May 12 2009 - 01:07:22 CDT

Thank you Eric and Joshua! It's what I need. I have a quite large DCD file
(more than 10 GB), so I will do it frame by frame. Can I save the unwrapped
atoms to a new DCD file?

Fred

On Tue, May 12, 2009 at 12:49 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

> You can choose not to wrap the system coordinates during the simulation,
> but keeping the periodic boundary conditions in place. The options in the
> namd script are "wrapall" and "wrapwater" I believe.
>
> You might also try unwrapping your existing trajectory using PBCtools:
>
> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> -Eric
>
> On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:
>
> Hi All,
>
> I have a question that can be simplified like this:
>
> Suppose there's a cube with lots of particles/atoms. The boundary is
> periodic and only Lennard Jones force field is in the system. All atoms are
> moving with random velocities. The velocity of the center of mass could not
> be zero. I have a common DCD file with coordinates of all atoms. My question
> is: how to get the displacement of all atoms?
>
> I cannot just simply subtract the coordinate of one atom from the
> coordinate of the same atom in the previous frame. Supposing the
> cube has 200 edge length and the center is (0,0,0). If a atom at the
> position (99, 0, 0) moves to the position (-99, 0, 0), the displacement
> could be either 2 or -198 because of the periodic boundary. The absolute
> coordinate could be (102, 0, 0), but in the DCD file it's (-99, 0, 0). It
> makes the displacement calculation impossible.
>
> So I was wondering if there are any ways with which NAMD can output a
> "modified" DCD file with absolute coordinates. Thank you!
>
> Have a nice day!
>
> Fred
>
>
> Eric H. Lee
>
> Medical Scholars Program
>
> Theoretical and Computational Biophysics Group, UIUC
>
> ericlee_at_ks.uiuc.edu
>
>

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