AMBER Archive (2008)

Subject: AMBER: a question about matrix command?

From: TaoPaul (paultao2008_at_hotmail.com)
Date: Tue Sep 02 2008 - 20:01:04 CDT

Dear all

When I learnt "matrix" command in ptraj to calculate distance matrix using "byres" I noted the

diagonal element was not zero(The similar situation was found using "bymask" . Then I read the

manual and it said "byres calculates the average for each residue". It is ambiguous and I want to

know the exact formula or expression and the physical meaning of this "average"(It seems don't like

the distance btween residual geometry centres). Could somebody help me? Thanks a lot!

Jin Tao

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