Re: [AMBER] cpptraj crosscorr command

From: Daniel Roe <>
Date: Thu, 4 Jun 2015 10:00:39 -0600


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.


On Wed, Jun 3, 2015 at 5:53 PM, Gard Nelson <> 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 …
> matrix name dstmtx dist <mask1> <mask2>
> go
> runanalysis crosscorr 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
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 04 2015 - 09:30:04 PDT
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