How do I generate distance matrices for specific frames in trajectory with GROMACS g_mdmat?

09 September 2015 1 6K Report

I would like to generate individual and mean distances for a trajectory using g_mdmat from GROMACS. That is, I have a list of time points in the simulation (which are not interspersed at a regular interval) that I wish to use to calculate distance matrices with. I can't find any option in the g_mdmat options list that can allow me to do this. Is there any way I can accomplish this?

Second, I wish to have access to the numerical values of the matrix but the .xpm output format is not easily parseable, is there a way to have access to the distance values produced by g_mdmat?

Thank you!

Justin Lemkul

This is what the g_mdmat -frames option does. Alternatively, dump out whatever frame(s) you want with trjconv -dump and analyze them individually.

The only way to get raw numbers is to write a simple parser that uses the information in the .xpm header to translate the symbols back to values.

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