I performed the trajectory analysis of my protein in different time intervals using g_mdmat program of gromacs. From user manual I came to know this program is use to Identify the spinning motion of different substructures ( beta sheet, helix) of protein. I have tried to search the related references but not able to find the same. Please provide me the related paper, literature or the way to evaluate the comparative study of different time interval of the trajectory.
Thank you very much
g_mdmat doesn't tell you about secondary structure. It provides a minimum-distance matrix between the residues in the selected group. I doubt there's a reference for such a program as it is not any sort of unique algorithm, it's just a distance calculation that just about any software can perform.
Your are right sir, after generating that matrix only we can generate the a map using xpm2ps a in-billed program of gromacs. This map having a diagonal line of minimum distance. Now I am searching a suitable reference for same.
Thanking you
As I said, there is no reference. Anything that requires citing would be printed by Gromacs in an obvious "PLEASE CITE" block.
What g_mdmat does is a trivial calculation, one that wouldn't merit even peer review; the program loops over all atoms in two loops with indices i and j, calculating the distance between all of them. The minimum distance is determined and assigned as the minimum distance between residues.
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