AMBER Archive (2009)

Subject: [AMBER] DCCM

From: Raja Pandian (
Date: Tue Jul 07 2009 - 06:05:20 CDT

Dear Amber user,

I would like to do the Dynamic Cross Correlation Map (DCCM) analysis.
Searching AMBER archive showed that similar questions have been posted
before but no answer.

I have a question about the cross-correlation calculation using ptraj (Amber
9). I use the following input for ptraj:

matrix correl name ABC_corr @CA out ABC_corr.dat

My questions are;

1) Does the "correl" result give me the so-called "DCCM"? I noticed some
publications showed the across-correlation map that was obtained form ptraj,
it seems to me they never use the term DCCM.

2) How can I plot the correlation matrix map (ABC_corr.dat)? Could you
please suggest me a graphic program for the correlation matrix data plot?

Thanks in advance for your suggestions.


Rajapandian. V
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