Re: [AMBER] : timecorr

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 9 Jul 2013 08:08:04 -0600

Hi,

The poorly-named 'crosscorr' command in CPPTRAJ will calculate the
Pearson product moment correlation coefficients between 2 or more data
sets. For example, using the input:

parm ../tz2.parm7
trajin ../tz2.nc
distance d1 :2 :12
radgyr rg :1-3 mass nomax
crosscorr d1 rg out d1rg.dat

You'll get a 2D matrix as output:

#crosscorr_00002
   1.000 1.000 0.0000
   1.000 2.000 -0.3105
   2.000 1.000 -0.3105
   2.000 2.000 0.0000

Here the first two numbers are the indices of the data sets
(corresponding to the order you gave to the crosscorr command), so the
first line reads 'correlation coefficient between data set 1 (d1) and
data set 1 is 0.0 (of course it should actually be 1.0, but since we
know that it's not actually calculated which is why it's reported as
zero), the second is correlation between data set 1 (d1) and data set
2 (rg), etc.

Note that the Pearson coefficient is also reported as part of output
from the 'corr' command (which computes time correlation functions for
non-vector data sets), e.g.:

  1: [corr d1 rg out cross.dat ]
    CORR: 101 elements, max lag 101
    CORRELATION COEFFICIENT d1 to rg IS -0.3105

Hope this helps,

-Dan

On Tue, Jul 9, 2013 at 6:34 AM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
> Dear David,
>
> Thanks for your answer.
> But I get the definition of correlation from our text book, Molecular
> Modeling Principles and Applications by Andrew R. Leach. And it's just the
> same as Pearson correlation (or at least the mathematical form). I have
> attached a screenshot of the definition to this letter.
>
>
> -----ʼԭ-----
> : David A Case [mailto:case.biomaps.rutgers.edu]
> ʱ: 201379 20:03
> ռ: AMBER Mailing List
> : Re: [AMBER] timecorr
>
> On Tue, Jul 09, 2013, Hongyi WU wrote:
>>
>> The function timecorr in AmberTools 13 will return squared correlation
>> r^2, right?
>
> No: the "time correlation" [C(t)] is unreleated to the Pearson (linear)
> correlation function (which it sounds like you might be thinking of).
> C(t) is normalized such that C(0)=1; it is not the square of anything.
>
> Apologies if I am misunderstanding your question.
>
> ..dac
>
>
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue Jul 09 2013 - 07:30:04 PDT
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