VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 09 2021 - 16:11:52 CST

Hi,
  If what you're after is a list of atoms that are within 4A at each frame,
that will end up being a different result (and even a different number
of results) for each frame. That being the case, since VMD can't export a
trajectory with a time-varying numbers of atom coordinates, you'd have to
take a different approach, such as writing out a separate coordinate file
per-frame, or similar. This is how I've interpreted what you wrote below,
but perhaps you're asking for something different than I am describing.
In any case, a lot more detail would be required to get much further
assistance.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 08, 2021 at 04:19:50PM +0530, SYEDA SABIHA SULTANA LUBNA . wrote:
> Hi,
> Can someone please help me out with the analysis of my dcd file.
> I want a list of atoms that are within 4 angstroms of my CU2 ion
> throughout the trajectory. Representation wise I am getting the
> visualization state using the representation trajectory option but when I
> am trying to save the selection it is saving the same atom coordinates for
> all the frames.Â
> Thank you.
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-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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