From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Sun Aug 27 2017 - 08:13:39 CDT
Hello,
First, please ask a question for VMD in the VMD -mailing list and not NAMD (like now).
To your question:
Use: pbc wrap -all -compound res -center com -centersel protein
To wrap your whole system over all frames in the box, with your protein in the center of this and don’t split residue (if only some atoms are out if the box).
I would not recommend the snapshot “rendering” cause every change in the display, that could happen during “rendering” (like energy save with screen off), could be seen in the final movie. I would use tachyon or tachyon optix (if possible).
If you want to show more than just rolling through the frames, for example switching on/off some representations, I would use the mentioned UserAni:
http://www.ks.uiuc.edu/Research/vmd/plugins/vmdmovie/
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/userani/
Sincerely
Daniel Möller
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Daipayan Sarkar
Gesendet: Sonntag, 27. August 2017 05:56
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Movie in VMD
Hello,
In my simulations the protein moves but remains within the water box, however the entire system moves as a unit when analyzing the frames later in VMD. I would like to hold the protein and waterbox at the center of the display window and record the snapshots of the unfolding process. I will then use the snapshots (ppm) to make a movie.
Thanks,
Daipayan
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:35 CST