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

Mark Abraham mark.j.abraham at gmail.com
Sat Nov 8 16:52:44 CET 2014

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.


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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list