Re: Calculating displacement in a system with periodic boundary

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Tue May 12 2009 - 02:25:48 CDT

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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