AMBER Archive (2009)

Subject: [AMBER] What is the meaning of "rms first *"

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Jul 30 2009 - 22:49:17 CDT


Dear Sir/Madam,

 

Should we expect the rotation and translation motion of whole system removed by "rms first *" command in PCA analysis? What is the * stands for?

 

If not, what should we do to remove the rotation and translation motion of the system before doing PCA analysis?

 

Best regards and many thanks in advanced,

 

Cat

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