**From:** Fred (Rui FENG) (*fengruifree_at_gmail.com*)

**Date:** Mon May 11 2009 - 23:26:21 CDT

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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

**Next message:**Joshua Adelman: "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Jerome Henin: "Re: soft-core FEP in namd 2.7b"**Next in thread:**Joshua Adelman: "Re: Calculating displacement in a system with periodic boundary"**Reply:**Joshua Adelman: "Re: Calculating displacement in a system with periodic boundary"**Reply:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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