Trajectories with non-constant atom list

Feature Requests item #1865909, was opened at 2008-01-07 06:39
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: Trajectories with non-constant atom list

Initial Comment:
I read the following in the To Do page: “Animation / vibrations: The best way may be to use OBMol conformation support, and simply rotate through the list of conformers. Essentially these just supply different sets of coordinates for the same set of atoms – useful for molecular dynamics (trajectories/reactions) or vibrations.”

I’d like to ask you to consider making it more general from the start, by not assuming that the number of atoms in each “frame” is constant (or that the list of atoms is the same for each frame): this is a common assumption in most molecular viewers, and is widely inappropriate for many types of molecular simulations (like Grand Canonical Monte Carlo). In fact, the VMD developers have now (IIUC) the greatest difficulty in removing this constraint because it is omnipresent in their code.

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