VMD-L Mailing List

From: Miguel Caro (miguel.caro_at_aalto.fi)
Date: Fri Oct 27 2017 - 08:43:14 CDT

Dear Joshua and Ashar,

Joshua's suggested solution works perfectly for me, get matrices in
preferred view, then apply them to everything else.

Thanks for your help,

Miguel

On 2017-10-26 22:41, Ashar Malik wrote:
> 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
> <mailto: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
> <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><mailto:mcaroba_at_gmail.com
> <mailto:mcaroba_at_gmail.com>>
> Work: miguel.caro_at_aalto.fi
> <mailto:miguel.caro_at_aalto.fi><mailto:miguel.caro_at_aalto.fi
> <mailto:miguel.caro_at_aalto.fi>>
> Websites:
> http://mcaroba.dyndns.orgaVgNcaIhYwr08gRItn0EVNTvoDUn2GSpboK2DKsL0%26s%3DvrPkFhrDRUdkxZX9G_mb3cAUXrGAYnj8QOikdrgTSEI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C52eeaf35ce85424fd17408d51c924e90%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636446337067005692&sdata=y5kIqDMOdhdIJhOPaoMHYitEcvhhxUqllPuX7RTRB%2Bc%3D&reserved=0
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__mcaroba.dyndns.org%26d%3DDwMCaQ%26c%3D8hUWFZcy2Z-Za5rBPlktOQ%26r%3Df0N5v4NY00lzag1jzuVkui7_420G9K7DR41QSpC55bU%26m%3DKBaVgNcaIhYwr08gRItn0EVNTvoDUn2GSpboK2DKsL0%26s%3DvrPkFhrDRUdkxZX9G_mb3cAUXrGAYnj8QOikdrgTSEI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C52eeaf35ce85424fd17408d51c924e90%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636446337067005692&sdata=y5kIqDMOdhdIJhOPaoMHYitEcvhhxUqllPuX7RTRB%2Bc%3D&reserved=0>>
> http://dospt.org0EVNTvoDUn2GSpboK2DKsL0%26s%3DnuWZs9rOLuQQF-bcY2qBCH3WCJa9MMdLZncfUGZAKfI%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C52eeaf35ce85424fd17408d51
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>  c924e90%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636446337067005692&sdata=7ZdD2PGsXvkqyAB%2FMzWDK%2F94g0SRgXyCiYy3qo22jdo%3D&reserved=0>
>
> 

-- 
*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*
Work: *miguel.caro_at_aalto.fi*
Websites: http://mcaroba.dyndns.org http://dospt.org