**From:** BIN ZHANG (*zhngbn_at_gmail.com*)

**Date:** Tue May 12 2009 - 02:25:48 CDT

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

You can use bigdcd script in the library : http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/

Bin

On May 11, 2009, at 11:37 PM, Fred (Rui FENG) wrote:

*> 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
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*> 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>
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*> wrote:
*

*> Yes, from the VMD File menu once you've finished unwrapping it.
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*>
*

*> On May 12, 2009, at 1:07 AM, Fred (Rui FENG) wrote:
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*>
*

*>> Thank you Eric and Joshua! It's what I need. I have a quite large
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*>> DCD file (more than 10 GB), so I will do it frame by frame. Can I
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*>> 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>
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*>> wrote:
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*>> You can choose not to wrap the system coordinates during the
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*>> simulation, but keeping the periodic boundary conditions in place.
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*>> The options in the namd script are "wrapall" and "wrapwater" I
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*>> believe.
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*>>
*

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

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

*>> -Eric
*

*>>
*

*>> On May 11, 2009, at 11:26 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
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*>>> is periodic and only Lennard Jones force field is in the system.
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*>>> All atoms are moving with random velocities. The velocity of the
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*>>> center of mass could not be zero. I have a common DCD file with
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*>>> coordinates of all atoms. My question is: how to get the
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*>>> 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
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*>>> the position (99, 0, 0) moves to the position (-99, 0, 0), the
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*>>> displacement could be either 2 or -198 because of the periodic
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*>>> boundary. The absolute coordinate could be (102, 0, 0), but in the
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*>>> DCD file it's (-99, 0, 0). It makes the displacement calculation
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*>>> impossible.
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*>>>
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*>>> So I was wondering if there are any ways with which NAMD can
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*>>> output a "modified" DCD file with absolute coordinates. Thank you!
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*>>>
*

*>>> Have a nice day!
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*>>>
*

*>>> Fred
*

*>>
*

*>> Eric H. Lee
*

*>> Medical Scholars Program
*

*>> Theoretical and Computational Biophysics Group, UIUC
*

*>> ericlee_at_ks.uiuc.edu
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*>>
*

*>>
*

*>
*

*> Eric H. Lee
*

*> Medical Scholars Program
*

*> Theoretical and Computational Biophysics Group, UIUC
*

*> ericlee_at_ks.uiuc.edu
*

*>
*

*>
*

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

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