Re: Calculating displacement in a system with periodic boundary

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Tue May 12 2009 - 02:52:49 CDT

Thank you! I'll try.

On Tue, May 12, 2009 at 3:25 AM, BIN ZHANG <zhngbn_at_gmail.com> wrote:

> 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 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?
>>
>> 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 namd script are "wrapall" and "wrapwater" I believe.
>>>
>>> You might also try unwrapping your existing trajectory using PBCtools:
>>>
>>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>>
>>> -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 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
>>>
>>>
>>> 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
>>
>>
>
>

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