[gmx-users] dynamic cross-correlation maps and older gromacs binaries

[Mark Abraham]

On Sat, Nov 8, 2014 at 12:19 PM, Rethi Madathil <madathir at gmail.com> wrote:

> Dear All,
>
> I am interested in generating dynamic cross-correlation maps to show the
> correlated and anti-correlated motion of bound and unbound protein.
>
> (for the reference see (e.g
>
> http://www.pnas.org/content/suppl/2013/06/18/1309755110.DCSupplemental/sapp.pdf
> Fig S10). See the image below
>
> However g_correlation will work with only gromacs-3.3 as the developers
> have confirmed it. The develops suggested to older gromacs version as
> g_correlation can still take gromacs4.5 .xtc files. I tried to download the
> old gromacs binaries but there seems to be problem.
>
> I would appreciate if someone can shed some light on
>
> 1) if older binaries are available and where to download them
>

If Google doesn't know, nobody does! Get the source and build it. IIRC 3.3
had build instructions in the tarball.

Mark

2) if there any other alternative ( I know modified g_covar by Ran Friedman
> is there but that is also an old program and will not work newer gromacs
> version)
>
>
> 3) can we generate cross-correlation map by using g_covar by providing the
> option -ascii and using the dat file generated to plot these maps in
> matlab. Does anyone have some matlab scripts to do that.
>
> If anyone know better method, tips, comments/suggestion that would be
> highly appreciated.
>
> Regards,
>
> Madathil
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