Perfect, thanks Dan.
On 6/4/15, 11:00 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>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,
>> >
>> > Iım sure there is something very basic that Iım missing, but for the
>> > life of me, I canıt 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 isnıt written.
>> >
>> > The point of this is to determine the difference (if any) between
>> > running crosscorr on a distance matrix, and running the ³matrix
>>correl²
>> command?
>> > Any explanations adding to whatıs 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
>> (801) 585-6208 (Fax)
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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)
>_______________________________________________
>AMBER mailing list
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>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Jun 04 2015 - 11:30:04 PDT
