[gmx-users] Correlation Matrix Calculation

[Arneh Babakhani]

Yes, I have seen this, had trouble compiling it.  Does it matter what
version of gromacs you're trying to compile it with?

> Hi,
>
>
> On Friday, 31. August 2007 05:14, Arneh Babakhani wrote:
>> Can anyone briefly recommend a procedure for calculating the correlation
>> matrix (not the diagonalized covariance matrix, as done by g_covar) of a
>> specified group?
>>
>> In particular, I'm looking to calculate the covariance matrix, as
>> specifed
>> in the Karplus paper (Proteins: Vol 11:205-217, 1991), where each entry
>> of
>> the matrix is defined as the correlation between the i-th and j-th atom:
>>
>> c_ij = <delta r_i> <delta r_j>
>>
>> where delta r is the deviation of i from its average position, averaged
>> over the ensemble.
>>
>> Or, is there a way to use g_covar and suppress the diagonalization step,
>> so as to obtain only the translation correlation matrix??? (I couldn't
>> find anything to this effect in the manual).
>
>
> take a look at Generalized Correlation for Biomolecular Dynamics from
> Lange
> and Grubmueller:
>
> http://www.mpibpc.gwdg.de/groups/grubmueller/start/people/olange/gencorr.html
>
>>
>> Much thanks,
>>
>> Arneh
>
> greetings,
>
> Florian
>
>
> --
> -------------------------------------------------------------------------------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Telephone:  	+49(0) − 9131 − 85 26581
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
> -------------------------------------------------------------------------------
>