Calculating displacement in a system with periodic boundary

From: Fred (Rui FENG) (
Date: Mon May 11 2009 - 23:26:21 CDT

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!


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