AMBER Archive (2008)

Subject: Re: AMBER: matrix correl

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Wed Feb 20 2008 - 11:35:30 CST

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On Feb 20, 2008 6:22 PM, Ibrahim Moustafa <I.moustafa_at_psu.edu> wrote:
> 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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-- 
mvh Lars Skjærven
Institutt for Biomedisin
Universitetet i Bergen
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