AMBER Archive (2004)

Subject: AMBER: ptraj and PCA

From: J Pang (JXP251_at_bham.ac.uk)
Date: Wed Oct 06 2004 - 05:54:17 CDT

Dear Amber Users,
I am at the moment trying to use ptraj to perform principal component analysis (PCA). Could anyone please give me an ptraj input example and explain a bit the overall processure. I read the Amber8 manual. It seems all the command under “Correlation and fluctuation facility” like “matrix” and “analyze matrix” could do it but I didn't quite figure out how it works. Another problem is I only have Amber7. Is it possible to get an Amber8 version ptraj?
Thanks a lot in advance.

Jiayun

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