[gmx-users] Probability contact map from g_mdmat

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 13 00:10:21 CET 2010

On 13/11/2010 6:30 AM, Ali Naqvi wrote:
> Dear All,
> I was playing around with g_mdmat to try and obtain a probability 
> contact plot instead of a mean plot or a frame dump, where it would 
> count the number of times a distance would occur between a range eg. 
> 0-0.4nm. This way the map would show the contact, as well as the 
> propensity to form that contact, relative to the covalent bonds shown 
> on the diagonal. Anyway this would be more important to me than a 
> means plot. I have searched the literature and this forum for "contact 
> map gromacs" keywords without results except for a conversion from xpm 
> to numbers script and a script that returns the various contacts 
> g_mdmat found.
> Hence, I wanted to know if someone has done this on their own, so I 
> won't reinvent. If not, I will modify the source and upload it to the 
> user contribution page. Let me know.

Do be sure that you can't get what you want from cunning use of some of 
the other tools, e.g. g_bond, g_dist or g_mindist.


More information about the gromacs.org_gmx-users mailing list