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

[Ebert Maximilian]

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? 

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?

Thanks,

Max

> On Mar 23, 2015, at 9:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
> 
> -- 
> ==================================================
> 
> 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
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.