[gmx-users] Re: Cross-correlation maps

James Starlight jmsstarlight at gmail.com
Fri Aug 24 08:51:43 CEST 2012

up :)
It's appeared two additional questions.

1) In addition to the pca's cross-correlation maps I wounder to know
about possibility of calculation of such cross-correlation's from the
trajectories indirectly without calculation of the covariance

2) is there any way to calculate degree of fluctuations of side-chains
( degree of  torsion's dynamics) from the different trajectories and
to compare it ?
E.g I have one protein in two different (apo and holo) forms. I've
calculated two trajectories for both structures and observed different
degree of dynamics in case of each structure ( e.g fluctuations in
case of apo form were  more frequent than in case of liganded form).
IS there any way to direct mesure and comprison of such side-chain's
dynamics for two trajectories?


2012/8/15, James Starlight <jmsstarlight at gmail.com>:
> Dear Gromacs users!
> I want to obtain Cross-correlation maps ( for indication of the
> cross-correlated fluctuations of the residues).
> The example of such maps can be found here
> http://pubs.acs.org/doi/abs/10.1021/ja076046a
>  I found that modificied version of the G_covar from users
> contributions can do such things. But because of the older version of
> that program (3.3.3) I've obtained the below error using it with 4.5.5
> gromacs
> Reading file md_GO.tpr, VERSION 4.5.5 (single precision)
> -------------------------------------------------------
> Program g_covar_mod, VERSION 3.3.3
> Source code file: tpxio.c, line: 1192
> Fatal error:
> reading tpx file (md_GO.tpr) version 73 with version 40 program
> -------------------------------------------------------
> Is there newest versions of the G_covar for such things or
> alternativelly any others ways to calculate such correlations maps ?
> Thanks for help
> James

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