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

[Ebert Maximilian]

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? 

Thank you very much,

Max 


> On Mar 12, 2015, at 8:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 3/12/15 6:20 PM, Ebert Maximilian wrote:
>> Dear list,
>> 
>> I am looking for a tool in gromacs to generate a map of residues pairs to indicate wether the dynamic/movement is correlated or anti correlated. Which tool is able to generate such an output?
>> 
> 
> gmx covar will plot the covariance matrix for all atom pairs (3N x 3N), but you can map that to residues.
> 
> -Justin
> 
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> Justin A. Lemkul, Ph.D.
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