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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 4 Jun 2015 12:00:56 -0600

On Thu, Jun 4, 2015 at 11:44 AM, Gard Nelson <Gard.Nelson.nantbio.com>

wrote:

*>
*

*> 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?
*

*>
*

Unfortunately no, although you could probably script something up using

multiple 'distance' commands (or if you like python you could try using

pytraj, a python front-end to cpptraj: https://github.com/pytraj/pytraj).

*> 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...
*

*>
*

It's actually calculating a normalized covariance matrix, where each matrix

element is the normalized covariance between atomic vectors Vi and Vj:

Mij = (<Vi * Vj> - <Vi> * <Vj>) / sqrt( (<Vi^2> - <Vi>^2)(<Vj^2> - <Vj>^2) )

See this publication for an early example of its use and definition:

http://www.ncbi.nlm.nih.gov/pubmed/7563068

-Dan

*>
*

*> Thanks for your help,
*

*> 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 …
*

*> >
*

*> > 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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*

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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
*

*> (801) 585-6208 (Fax)
*

*> _______________________________________________
*

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*

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*

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

*> CONFIDENTIALITY NOTICE
*

*> This e-mail message and any attachments are only for the use of the
*

*> intended recipient and may contain information that is privileged,
*

*> confidential or exempt from disclosure under applicable law. If you are not
*

*> the intended recipient, any disclosure, distribution or other use of this
*

*> e-mail message or attachments is prohibited. If you have received this
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*> e-mail message in error, please delete and notify the sender immediately.
*

*> Thank you.
*

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*

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*>
*

Date: Thu, 4 Jun 2015 12:00:56 -0600

On Thu, Jun 4, 2015 at 11:44 AM, Gard Nelson <Gard.Nelson.nantbio.com>

wrote:

Unfortunately no, although you could probably script something up using

multiple 'distance' commands (or if you like python you could try using

pytraj, a python front-end to cpptraj: https://github.com/pytraj/pytraj).

It's actually calculating a normalized covariance matrix, where each matrix

element is the normalized covariance between atomic vectors Vi and Vj:

Mij = (<Vi * Vj> - <Vi> * <Vj>) / sqrt( (<Vi^2> - <Vi>^2)(<Vj^2> - <Vj>^2) )

See this publication for an early example of its use and definition:

http://www.ncbi.nlm.nih.gov/pubmed/7563068

-Dan

-- ------------------------- 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 (801) 585-6208 (Fax) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Jun 04 2015 - 11:30:03 PDT

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