**From:** Joshua Adelman (*jadelman_at_berkeley.edu*)

**Date:** Mon May 11 2009 - 23:44:23 CDT

**Next message:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**In reply to:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**Next in thread:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

If you had perfect knowledge of every atom at every time step of the

simulation I imagine that you could could calculate the path length by

checking for the case when a particle goes through the boundary and

comes in the opposite side. The other option is to re-run the

simulation and don't wrap the coordinates. It will look like your

system is drifting apart when you look at the dcd, but the PBC should

be applied when NAMD calculates the forces. You could then post-

production re-wrap the coordinates using the PBC tools in VMD.

Josh

On May 11, 2009, at 9:26 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
*

------------------------------------------------------------------------------------------------------

Joshua L. Adelman

Biophysics Graduate Group Lab: 510.643.2159

218 Wellman Hall Fax: 510.642.7428

University of California, Berkeley http://nature.berkeley.edu/~jadelman

Berkeley, CA 94720 USA jadelman_at_berkeley.edu

------------------------------------------------------------------------------------------------------

**Next message:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**In reply to:**Fred (Rui FENG): "Calculating displacement in a system with periodic boundary"**Next in thread:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:52:46 CST
*