AMBER Archive (2004)

Subject: AMBER: Correl in Amber8: Diagonal elements not 1?

From: Bimo Ario Tejo (bimo7_at_gmx.de)
Date: Thu Jul 15 2004 - 06:47:43 CDT

Dear Amber users,

Does anyone have experience with correlation facility in Amber8? The
residue-residue correlation map of "matrix" command has diagonal elements
are not 1! It's weird because I thought the residue will move correlated
with itself during the simulation; thus, the correlation should be 1.

Here is my input file for ptraj:

trajin corr500.crd.gz
center :1-534 mass origin
image origin center
rms first mass out rmsh.dat :1-534
matrix correl name corr :1-534 out dccm byres mass

And here is a part of the output file (534x534 matrix, I took only 10x10
matrix):

  0.89 0.66 0.37 0.29 0.13 -0.03 -0.24 -0.27 -0.20 -0.08
  0.66 0.89 0.58 0.42 0.25 0.03 -0.07 -0.19 -0.12 -0.08
  0.37 0.58 0.75 0.66 0.47 0.25 0.24 0.07 0.14 0.12
  0.29 0.42 0.66 0.90 0.73 0.47 0.40 0.23 0.32 0.32
  0.13 0.25 0.47 0.73 0.85 0.60 0.53 0.38 0.44 0.39
 -0.03 0.03 0.25 0.47 0.60 0.77 0.65 0.61 0.57 0.56
 -0.24 -0.07 0.24 0.40 0.53 0.65 0.90 0.71 0.59 0.46
 -0.27 -0.19 0.07 0.23 0.38 0.61 0.71 0.90 0.77 0.68
 -0.20 -0.12 0.14 0.32 0.44 0.57 0.59 0.77 0.93 0.80
 -0.08 -0.08 0.12 0.32 0.39 0.56 0.46 0.68 0.80 0.85

Any hints?

Best regards,
Bimo

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