[gmx-users] minimum distance matrix and secondary structure

[Q.Z.]

Dear All,
 I heard that the average minimum distance matrix can be used to 
identify secondary and tertiary structure and then can be used to 
monitor the changes of these structural elements with time.
 Now I have used g_mdmat to generate the NxN matrix. How do I visually 
identify the these structures on the contour map, in terms of the 
location of alpha-helix, beta-sheet, etc? Thanks.

Q. Zou, PhD