AMBER Archive (2007)

Subject: AMBER: Question about ptraj matrix correl command

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Oct 31 2007 - 01:18:55 CST

Dear Sir/Madam,

We are doing a simulation for a protein for 1 ns in 10 separated files, i.e. I got ten mdcrd files at the end of the simulation.

I could like to study the correlated movement between residue 100 with the rest of the proteins afterall. I tried two different approaches.

First approach is:

trajin 1.mdcrd.gz
rms previous
matrix correl name c1_at_CA out 1.dat byres

then, I do the same analysis for the 2.mdcrd.gz .....10.mdcrd.gz separately. Then, the column which corresponding to the correlation coefficient of residue 100 and the rest of the protein residues were averaged in excel.

The second approach is:

trajin 1.mdcrd.gz
trajin 2.mdcrd.gz
...
trajin 10.mdcrd.gz
rms previous
matrix correl name c1_at_CA out 1to10.dat byres

Then, I read the column corresponding to the correlation coeficient of residue 100 and the rest of the protein residues.

However, totally diferent results were obtained. Could you please kindly comment why different results were obtained, and which one is correct?

Best regards and many thanks in advanced

Cat.
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