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

Rethi Madathil madathir at gmail.com
Sat Nov 8 12:19:20 CET 2014

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
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

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

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.



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