Re: [AMBER] Reonstructing frames from PCA projection

From: Daniel Roe <>
Date: Mon, 20 Jul 2020 10:43:58 -0400


It's not clear to me exactly what you want to do. If you want to
visualize how coordinates change along a certain eigenvector you can
use the 'modes trajout' analysis command to create a
pseudo-trajectory. If you want to extract frames that correspond to a
particular projection value, you can first use the 'projection' action
command to calculate the projection along certain eigenvectors, then
the 'filter' action to only allow frames that match certain projection
values to be written by a subsequent 'trajout' statement.

Let me know if you have more questions. Good luck!


On Fri, Jul 17, 2020 at 11:24 AM Michael F. Bruist
<> wrote:
> I would like to reconstruct frames using selected projections obtained from PCA analysis. If there is no direct command for this, I could do it with the appropriate vector/matrix math, but I cannot find appropriate commands for that either.
> Mike Bruist, University of the Sciences
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Received on Mon Jul 20 2020 - 08:00:03 PDT
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