Re: Calculating displacement in a system with periodic boundary

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Tue May 12 2009 - 01:37:58 CDT

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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