[gmx-users] What does g_rama calculate?

Justin Lemkul jalemkul at vt.edu
Sun Aug 31 17:30:48 CEST 2014

On 8/31/14, 11:27 AM, Dawid das wrote:
> 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?

There is a data point for each residue in each frame.  You can easily tell this 
by examining the contents of the file, and also by noticing there are probably a 
ton more data points than there are residues, so it can't be averages.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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