From: Vermaas, Joshua (
Date: Thu Oct 26 2017 - 12:49:41 CDT

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, 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. :)


On 10/26/2017 10:55 AM, Miguel Caro wrote:


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?



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:<>
Websites: http://mcaroba.dyndns.orgaVgNcaIhYwr08gRItn0EVNTvoDUn2GSpboK2DKsL0%26s%3DvrPkFhrDRUdkxZX9G_mb3cAUXrGAYnj8QOikdrgTSEI%26e%3D&> http://dospt.org0EVNTvoDUn2GSpboK2DKsL0%26s%3DnuWZs9rOLuQQF-bcY2qBCH3WCJa9MMdLZncfUGZAKfI%26e%3D&>