[gmx-users] What does g_rama calculate?

Dawid das addiw7 at googlemail.com
Sun Aug 31 17:27:23 CEST 2014

Dear Gromacs experts,

I am wondering what I actually see when I plot output from g_rama. When I
run it like this:

g_rama -f 3ldj-npt-md.trr -s npt-md.tpr -o 3ldj-npt-rama.xvg

I plot the output using:

xmgrace 3ldj-npt-rama.xvg

Now I see Ramachandran plots with squares and phi and psi angles  on axes.
So what these points actually show? Are these average values for each
residue or are these all phi and psi combinations for all residues all
along the trajectory?

Best wishes,

Dawid Grabarek

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