[gmx-users] Correlation of dynamics between pairs of residues

[Justin Lemkul]

On 3/24/15 8:21 AM, Ebert Maximilian wrote:
> Thanks for taking the time to answer. However, I don’t really understand why having the same axis basically (so from -2 to 2 nm^2 for example) would defy the purpose of the analysis. Could you explain that?
>

Perhaps "defeats the purpose" wasn't the right way to say it.  But simply 
plotting the covariance matrices with arbitrary min/max is just an aesthetic 
thing, so it's not really functional.  Hence why no one has coded that.

> I guess your hint with open source is that i could check how the covara is calculated and do it on my own using the .dat ascii file? Do you know where the function is in the code?
>

src/gromacs/tools/gmxana/gmx_covar.c

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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