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

**Date:** Tue May 12 2009 - 01:37:58 CDT

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

My DCD file is too large to be loaded to the memory. So I have to process it

frame by frame. Are there any scripts that can save the coordinates to a DCD

file frame by frame? Thank you.

On Tue, May 12, 2009 at 2:15 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu> wrote:

*> 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?
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*>
*

*> 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
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*>> namd script are "wrapall" and "wrapwater" I believe.
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*>>
*

*>> You might also try unwrapping your existing trajectory using PBCtools:
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*>>
*

*>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
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*>>
*

*>> -Eric
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*>>
*

*>> On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:
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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
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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
*

*>> be zero. I have a common DCD file with coordinates of all atoms. My question
*

*>> is: how to get the displacement of all atoms?
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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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*>>
*

*>> 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!
*

*>>
*

*>> 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
*

*>
*

*>
*

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

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