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

[Justin Lemkul]

On 3/23/15 3:43 PM, Ebert Maximilian wrote:
> Hi Justin,
>
> thanks for your answer. gmx covar is really helpful and does what I was
> looking for.I have 3 replicates of the simulation and wanted now to compare
> the covariance and maybe calculate an average of the 3. The covara output is
> what I am looking for but the file created is more or less a picture and not
> really the data anymore. In addition, the scale of + and 0 nm^2 is not the
> same in each of the 3 output of the simulation so it is hard to compare. Is
> there a way to set min and max values for nm^2? Can I find an explanation how
> the data was calculated using the dat file i can generate using gmx covar?
>

One approach would be to simply pool the trajectories and run gmx covar once. 
That will do the analysis over all of your trajectories and you no longer have 
this issue.  But there is no way to control what the min and max values are; 
that sort of defeats the purpose of the analysis.

As for the explanation, that's why GROMACS is open source :)

-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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