# Re: [AMBER] cpptraj crosscorr command

From: Gard Nelson <Gard.Nelson.NantBio.com>
Date: Thu, 4 Jun 2015 17:44:38 +0000

Thanks Dan,

That makes perfect sense. For some reason, I was thinking that instead of an average, the "matrix dist" command would produce an M x N x S matrix, where M and N are the atom indicies and S is the number of steps. Given that that isn't how the "correl" command behaves, I should have known better. Out of curiosity, is there any way to write such a distance matrix (M x N x S) from cpptraj?

Based on my (hurried) reading of the code, the "matrix correl" command seems to be calculating the same formula found on Wikipedia for the Pearson product-moment, (rhoX,Y = <(X - uX)(Y - uY)> / (sigmaX * sigmaY)) but between frames instead of between datasets as you explained. Is that correct? Is "dynamic cross correlation" referring to the Pearson product-moment, or is there some subtlety I'm missing? My googling hasn't returned much for it...

gard

-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Thursday, June 04, 2015 9:01 AM
To: AMBER Mailing List
Subject: Re: [AMBER] cpptraj crosscorr command

Hi,

This is a case of the error message in cpptraj being woefully inadequate.
The 'crosscorr' command (another terribly named command, I'm on a roll
today) calculates the Pearson product-moment correlation coefficients between 1D data sets and puts them in a matrix. So if you have 3 1D data sets (from e.g. the distance command) named d1, d2, and d3 you would get a matrix like so:

--- d1%d2 d1%d3
--- --- d2%d3
--- --- ---

where % in this case denotes the correlation calculation. Since you're only giving it 1 data set there's nothing to calculate correlation to (and if you did give it more data sets I suspect the code would segfault). The 'matrix correl' command calculates a "dynamic cross correlation matrix", the elements of which are the normalized covariance between atomic vectors.
In contrast, the elements of a distance matrix are simply the average distance between the two atoms.

Hope this clears some things up, let me know if you have more questions.
Thanks also for the report, cpptraj should do a better job trapping and giving information about this issue.

-Dan

On Wed, Jun 3, 2015 at 5:53 PM, Gard Nelson <Gard.Nelson.nantbio.com> wrote:

> Hi everyone,
>
> I’m sure there is something very basic that I’m missing, but for the
> life of me, I can’t figure out what it is. I want to run the crosscorr
> analysis and have tried every permutation of the following that I can think of.
>
> parm …
> trajin …
>
> dstmtx out crosscorr.dat
>
> Regardless of what I do, cpptraj tells me that the size of
> crosscorr_00001 is zero and the output file isn’t written.
>
> The point of this is to determine the difference (if any) between
> running crosscorr on a distance matrix, and running the “matrix correl” command?
> Any explanations adding to what’s contained in the manual would be
> appreciated.
>
> Thanks,
> gard
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Thu Jun 04 2015 - 11:00:02 PDT
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