AMBER Archive (2008)

Subject: AMBER: How to calculate RMSIP after PCA analysis by PTRAJ?

From: sychen (
Date: Wed Jun 04 2008 - 07:27:45 CDT

Dear all,
I need a program or script to calculate RMSIP (root-mean-square inner product)
between two sets of eigenvectors from PCA analysis by PTRAJ.
Such function appeared to be useful for comparing modes similarities
between two trajectories from different simulations after PCA calculation.
(rmsip of 1 indicates that the sets are identical, while a value of 0 indicates that the eigenvectors are orthogonal)

Thank you very much!

ps: Two articles referenced about the methodology of RMSIP are as follows:
1. de Groot, B. L.; vanAalten, D. M. F.; Amadei, A.; Berendsen, H. J. C. Biophys. J. 1996, 71 (4), 1707-1713.
2. de Groot, B. L.; Hayward, S.; van Aalten, D. M. F.; Amadei, A.; Berendsen, H. J. C. Proteins 1998, 31 (2), 116-127.

Best regards,

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