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

**Date:** Tue May 12 2009 - 01:07:22 CDT

**Next message:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Roman Petrenko: "namd-cuda-intel vs. namd-intel"**In reply to:**Eric H. Lee: "Re: Calculating displacement in a system with periodic boundary"**Next in thread:**Eric H. Lee: "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 ]

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,
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*> but keeping the periodic boundary conditions in place. The options in the
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*> namd script are "wrapall" and "wrapwater" I believe.
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*>
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*> You might also try unwrapping your existing trajectory using PBCtools:
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*>
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*> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
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*>
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*> -Eric
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*>
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*> On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:
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*>
*

*> Hi All,
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*>
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*> I have a question that can be simplified like this:
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*>
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*> Suppose there's a cube with lots of particles/atoms. The boundary is
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*> periodic and only Lennard Jones force field is in the system. All atoms are
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*> moving with random velocities. The velocity of the center of mass could not
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*> be zero. I have a common DCD file with coordinates of all atoms. My question
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*> is: how to get the displacement of all atoms?
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*>
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*> I cannot just simply subtract the coordinate of one atom from the
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*> coordinate of the same atom in the previous frame. Supposing the
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*> cube has 200 edge length and the center is (0,0,0). If a atom at the
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*> position (99, 0, 0) moves to the position (-99, 0, 0), the displacement
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*> could be either 2 or -198 because of the periodic boundary. The absolute
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*> coordinate could be (102, 0, 0), but in the DCD file it's (-99, 0, 0). It
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*> makes the displacement calculation impossible.
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*>
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*> So I was wondering if there are any ways with which NAMD can output a
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*> "modified" DCD file with absolute coordinates. Thank you!
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*>
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*> Have a nice day!
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*>
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*> Fred
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*>
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*>
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*> Eric H. Lee
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*>
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*> Medical Scholars Program
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*>
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*> Theoretical and Computational Biophysics Group, UIUC
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*>
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*> ericlee_at_ks.uiuc.edu
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*>
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*>
*

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