[gmx-users] Probability contact map from g_mdmat

Ali Naqvi mnaqvi at ryerson.ca
Fri Nov 12 20:30:43 CET 2010

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.

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