Re: [AMBER] Comparing trajectories

From: Thomas Cheatham <>
Date: Wed, 19 Jan 2022 21:16:26 +0000

As long as you have a 1:1 mapping among the atoms selected for the PCA; you want to do "combined PCA" so that the modes are equivalent in each (i.e. combine trajectories and separately project on each trajectory). I think there is a tutorial on but that site is hanging at the moment (I alerted the team).


From: Reza Khayat <>
Sent: Wednesday, January 19, 2022 2:04 PM
To: AMBER Mailing List
Subject: [AMBER] Comparing trajectories


I have a na´ve question. Is it possible to compare the conformational states that a protein complex can adopt under two different conditions? If I have a trajectory for each condition, can I do PCA for each condition and compare the PCA results? Thanks.

Best wishes,


Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
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Received on Wed Jan 19 2022 - 13:30:03 PST
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