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I'm wanting to use gmx sasa. I've done this on some residues I'm interested in analyzing. When I look at the output, I expect some value of $\pu{nm^2}$ or maybe $\pu{\unicode[.8,0]{x212B}^2}$. Instead, the .xvg file that is output has the following:

#   gmx_mpi sasa -f md_nojump.xtc -s md.tpr -n dyes.ndx -o gromacsSASA.xvg -odg gromacsSASADeltaG.xvg -or gromacsSASAAverage.xvg -tv gromacsSASAVolume.xvg -e 2010000 -pbc -rmpbc -probe 0.14 -ndots 24
# gmx sasa is part of G R O M A C S:
#
# Glycine aRginine prOline Methionine Alanine Cystine Serine
#
@    title "Solvent Accessible Surface"
@    xaxis  label "Time (ps)"
@    yaxis  label "Area (nm\S2\N)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Total"
      0.000   11.749
     10.000   11.430
     20.000   11.209
     30.000   11.114
     40.000   11.620
     50.000   11.810
     60.000   10.976
     70.000   11.592
     80.000   10.932
...

Here is a sample of what the atoms I'm interested. They are a part of a DNA-ligand type system. They are about 120 atoms total I'm looking at.

Molecules analyzed by gmx SASA Does anyone know what that area unit is? It looks something like (nm)(seconds^-2)(Newton^-1). This would not be an area unit if that's the case, so this doesn't make sense to me.

Or maybe it is nm^2/(number of dots)?. I think that might make sense, but the GROMACS documentation doesn't say. The paper they reference that talks about the algorithm doesn't give any kind of hints for units either.

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    $\begingroup$ +1. Can you show the whole output file? If it were to be nm/s^2/N, wouldn't we have / instead of \? Also the characters used for picoseconds are ps not pS so I would be surprised if seconds^2 were to use a capital s. Perhaps the S2 stands for "superscript 2". I think we need more information, such as your exact input and full output. Can you try this on a system where you know the area will be exactly 1 nm^2, and then see if that's what you get? $\endgroup$ Commented Mar 23, 2022 at 2:07
  • $\begingroup$ Exact Input is tricky since those files are big, but I'll edit to include a picture of the molecules I'm interested in, and some of the number outputs $\endgroup$ Commented Mar 23, 2022 at 20:45
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    $\begingroup$ Please include the input even if it's a few thousand characters. If it's beyond the site's limits, then please upload it to the "Modeling Matters" github repository in a folder named according to this question number (see the URL of your question). $\endgroup$ Commented Mar 23, 2022 at 20:49
  • $\begingroup$ The .xtc file is over 100MB so GitHub gave me some warning it won't be accepted. I don't think I can share that easily. $\endgroup$ Commented Mar 23, 2022 at 22:09
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    $\begingroup$ Can you compress it using xz -k -8 file.xtc in Linux? That's a beautiful picture by the way! I'm glad you added that!! $\endgroup$ Commented Mar 24, 2022 at 0:38

1 Answer 1

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The unit is actually $\pu{nm^2}$. What is written there is not is not specific to GROMACS, but to the plotting program it is using Xmgrace. \S denotes the start of superscript font, which ends when it encounters a \N.

If you pass this file as an input to Xmgrace, it should produce a plot of surface area ($\pu{nm^2}$) vs time ($\pu{ps}$).

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    $\begingroup$ +1. What a bizarre markup language. Matlab and matplotplib use TeX: ^2 and I think Techplot used HTML: <sup>2</sup>. Xmgrace just had to go ahead and make their own thing. $\endgroup$ Commented Mar 26, 2022 at 5:38
  • $\begingroup$ Very weird. Glad you could provide an answer! $\endgroup$ Commented Mar 28, 2022 at 20:02

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