[gmx-users] cross-correlations as a function of interatomic distance

[Tsjerk Wassenaar]

Hi,

Well, since interatomic distances are properties of single
conformations and fluctuation covariances/correlations are properties
of sets of conformations, it is simply impossible. You might plot the
covariances/correlations against the mean distances, if you feel you
must. Be sure to use the atomic fluctuations and not the
per-coordinate fluctuations.

Cheers,

Tsjerk

On Tue, Mar 16, 2010 at 7:34 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 16/03/2010 5:16 PM, shahab shariati wrote:
>>
>> Hi gromacs users
>>
>> After using g_covar for obtaining dynamic cross correlation map, how is
>> obtained cross-correlations as a function of interatomic distance?
>>
>> Thank you so much for any help!
>
> I'm not even sure whether "cross-correlations as a function of interatomic
> distance" makes sense. Perhaps you need to explain further what you mean.
> Writing out the maths of it may make it clear to you what it is you need to
> do with the output from g_covar.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist