AMBER Archive (2008)

Subject: RE: AMBER: matrix correl

From: Ibrahim Moustafa (I.moustafa_at_psu.edu)
Date: Wed Feb 20 2008 - 11:22:53 CST

Dear Amber Moderators,

This e-mail is bombarding me more than once a day. Could someone of the
moderators take care of this plz.

  Thanks,
Ibrahim

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David Beveridge
Sent: Saturday, February 16, 2008 4:09 AM
To: amber_at_scripps.edu
Subject: AMBER: matrix correl

Did this problem ever get diagnosed?

DLB

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

David L. Beveridge
University Professor
Chemistry Department and
Molecular Biophysics Program
Wesleyan University
Middletown, CT 06459
Ph 860 346 6768
Fx 860 346 2211

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