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From: Hongyi WU <why0713.sjtu.edu.cn>

Date: Sun, 21 Jul 2013 10:51:19 +0800

Daniel,

Sorry for my terribly late reply...

But how can I calculate the correlation between 2 vectors (e.g. 2 alpha

carbons) over a period of time, which I think is to calculate the

correlation between 2 matrix:

{{x1(1),y1(1),z1(1)},{x1(2),y1(2),z1(2)},...,{x1(t),y1(t),z1(t)}}

And

{{x2(1),y2(1),z2(1)},{x2(2),y2(2),z2(2)},...,{x2(t),y2(t),z2(t)}}

Hongyi

-----ÓÊ¼þÔ¼þ-----

·¢¼þÈË: Daniel Roe [mailto:daniel.r.roe.gmail.com]

·¢ËÍÊ±¼ä: 2013Äê7ÔÂ9ÈÕ 22:08

ÊÕ¼þÈË: AMBER Mailing List

Ö÷Ìâ: Re: [AMBER] ´ð¸´: timecorr

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.
*

*>
*

*>
*

*> -----ÓÊ¼þÔ¼þ-----
*

*> ·¢¼þÈË: David A Case [mailto:case.biomaps.rutgers.edu]
*

*> ·¢ËÍÊ±¼ä: 2013Äê7ÔÂ9ÈÕ 20:03
*

*> ÊÕ¼þÈË: AMBER Mailing List
*

*> Ö÷Ìâ: 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
*

*>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Sun, 21 Jul 2013 10:51:19 +0800

Daniel,

Sorry for my terribly late reply...

But how can I calculate the correlation between 2 vectors (e.g. 2 alpha

carbons) over a period of time, which I think is to calculate the

correlation between 2 matrix:

{{x1(1),y1(1),z1(1)},{x1(2),y1(2),z1(2)},...,{x1(t),y1(t),z1(t)}}

And

{{x2(1),y2(1),z2(1)},{x2(2),y2(2),z2(2)},...,{x2(t),y2(t),z2(t)}}

Hongyi

-----ÓÊ¼þÔ¼þ-----

·¢¼þÈË: Daniel Roe [mailto:daniel.r.roe.gmail.com]

·¢ËÍÊ±¼ä: 2013Äê7ÔÂ9ÈÕ 22:08

ÊÕ¼þÈË: AMBER Mailing List

Ö÷Ìâ: Re: [AMBER] ´ð¸´: timecorr

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:

of).

-- ------------------------- 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) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Jul 20 2013 - 20:00:03 PDT

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