# Re: Calculating displacement in a system with periodic boundary

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Tue May 12 2009 - 01:15:56 CDT

Yes, from the VMD File menu once you've finished unwrapping it.

On May 12, 2009, at 1:07 AM, Fred (Rui FENG) wrote:

> 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
>
>

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

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