VMD-L Mailing List

From: Lohry, David Patrick (dlohry_at_vols.utk.edu)
Date: Thu Apr 18 2024 - 12:14:52 CDT

I opened the RMSD Trajectory Tool and selected "Align" to the first frame. That appeared to work perfectly, and it was very quick.

Thank you for the response!
________________________________
From: Josh Vermaas <vermaasj_at_msu.edu>
Sent: Thursday, April 18, 2024 1:05 PM
To: Lohry, David Patrick <dlohry_at_vols.utk.edu>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: MD Videos and fixing the view into a certain perspective

Hi David,

Why not use something like the RMSD trajectory tool to align the structure on top of your region of interest? That way, that part of the system appears not to move, and you can maintain a fixed camera position.

-Josh

On 4/18/24 11:53 AM, Lohry, David Patrick wrote:
Hello,

I'm trying to create movies from molecular dynamics simulations. In some of these simulations, the complex might rotate many degrees out of view.

I would like to rotate and scale the molecule in Frame 0 and have it maintain that perspective through the entire simulation video. Perhaps one way is to have VMD fix itself on a certain residue or groups of residues to prevent rotation.

A manual based method might be where I export so many frames at once, stop it, re-rotate the molecule back into view, export more frames.

However, I can't seem to find out how to do that automatically. Is there a way in VMD to do this automatically?

Thank you!
David 

--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io