[gmx-users] What does g_rama calculate?

[Justin Lemkul]

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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