VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Oct 26 2017 - 14:41:59 CDT

After unwrap, perhaps use 'Align' with frame 0 as reference. Once all
frames in first chunk are aligned make first movie. Now the hacky bit.
>From the first chunk load frame 0 only.
Add the entire second trajectory to it. Align again (after unwrap if you
haven't unwrapped the entire trajectory i.e. all bits before). All frames
in second chunk will now align to the same reference as in 1st chunk/movie.
During the movie making part for 2nd chunk exclude frame 0 and make 2nd
movie for frames 1 through till the end. Repeat this process for all chunks.

Given that each chunk is aligned to frame 0 from first chunk I think view
centre should stay at one point. Since I just made this solution up right
now, I am only half sure that it will work. Do give it a try.

Hope this helps.

On Oct 27, 2017 07:41, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov> wrote:

> Hi Miguel,
>
> If you are happy with how the simulation is wrapped, but just want to make
> sure the camera is consistent, there are a set of matricies that you can
> set so that the camera is consistently placed between frames. See
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node142.html, but you'd
> basically lookup the center_matrix, rotate_matrix, and scale_matrix from a
> view that you like (molinfo top get x_matrix), and then apply that to the
> other trajectories *after* you load them. This is alot easier than
> back-calculating where the atoms need to go to deal with the moved camera.
> :)
>
> -Josh
>
> On 10/26/2017 10:55 AM, Miguel Caro wrote:
>
> Hello,
>
> I have a long trajectory file which I had to split into several chunks to
> avoid running out of memory. I want to make a video out of each chunk and
> then paste the videos together.
>
> When I load the trajectory chunks separately, the origin seems to shift
> with respect to the display. I suspect VMD centers the system on the
> display about the center of mass. Since the center of mass changes between
> chunks, the position of the origin with respect to the display is not
> preserved and the atoms are shifted from one video to the next.
>
> I want to be able to position the atoms consistently, so that the video
> transitions smoothly between its several pieces. In practice, I just need
> my origin in atomic coordinates to always appear in the same position in
> "display coordinates". How can I do this via scripting?
>
> Thanks,
>
> Miguel
>
> --
> Dr. Miguel Caro
> Academy of Finland Postdoctoral Researcher
> Department of Electrical Engineering and Automation,
> and COMP Centre of Excellence in Computational Nanoscience
> Aalto University, Finland
> Personal email: mcaroba_at_gmail.com<mailto:mcaroba_at_gmail.com>
> Work: miguel.caro_at_aalto.fi<mailto:miguel.caro_at_aalto.fi>
> Websites: http://mcaroba.dyndns.org.
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