GMX-SHAM(1)

💖 GMX-SHAM(1) — the GROMACS girlies' guide 💖

okay bestie, so this is gmx-sham from the GROMACS manual (section 1 of the manual, if you're keeping track 👑). It's the glow-up era version, and I'm gonna walk you through every single flag like we're sitting in the library at 2am with iced coffee. no cap.

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✨ NAME ✨

gmx-sham — Compute free energies or other histograms from histograms 🦋

✨ SYNOPSIS ✨

gmx sham [-f [<.xvg>]] [-ge [<.xvg>]] [-ene [<.xvg>]] [-dist [<.xvg>]]
         [-histo [<.xvg>]] [-bin [<.ndx>]] [-lp [<.xpm>]]
         [-ls [<.xpm>]] [-lsh [<.xpm>]] [-lss [<.xpm>]]
         [-ls3 [<.pdb>]] [-g [<.log>]] [-[no]w] [-xvg <enum>]
         [-[no]time] [-b <real>] [-e <real>] [-ttol <real>]
         [-n <int>] [-[no]d] [-[no]sham] [-tsham <real>]
         [-pmin <real>] [-dim <vector>] [-ngrid <vector>]
         [-xmin <vector>] [-xmax <vector>] [-pmax <real>]
         [-gmax <real>] [-emin <real>] [-emax <real>]
         [-nlevels <int>]

like, that's the whole vibe right there 💅

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🌸 DESCRIPTION 🌸

so gmx sham makes multi-dimensional free-energy, enthalpy and entropy plots. it reads one or more .xvg files and analyzes data sets. 🎀

the basic purpose of gmx sham is to plot Gibbs free energy landscapes (that's option -ls) by Boltzmann-inverting multi-dimensional histograms (that's option -lp) — but it can also make enthalpy plots (option -lsh) and entropy plots (option -lss). obsessed honestly. 😭 The histograms can be made for any quantities the user supplies, which is giving very customizable, very main character. ✨

A line in the input file may start with a time (see option -time) and any number of y-values may follow. Multiple sets can also be read when they are separated by & (option -n), and in this case only one y-value is read from each line. All lines starting with # and @ are skipped. bye bye comments 🫶

Option -ge can be used to supply a file with free energies when the ensemble is not a Boltzmann ensemble, but needs to be biased by this free energy. One free energy value is required for each (multi-dimensional) data point in the -f input. one per point. periodt. 💀

Option -ene can be used to supply a file with energies. These energies are used as a weighting function in the single histogram analysis method by Kumar et al. When temperatures are supplied (as a second column in the file), an experimental weighting scheme is applied. In addition the values are used for making enthalpy and entropy plots. 🍓

With option -dim, dimensions can be given for distances. When a distance is 2- or 3-dimensional, the circumference or surface sampled by two particles increases with increasing distance. Depending on what one would like to show, one can choose to correct the histogram and free-energy for this volume effect. The probability is normalized by r and r^2 for dimensions of 2 and 3, respectively. A value of -1 is used to indicate an angle in degrees between two vectors: a sin(angle) normalization will be applied. 💅

Note that for angles between vectors the inner-product or cosine is the natural quantity to use, as it will produce bins of the same volume. (lowkey a glow-up tip, not a suggestion to fight the math 🧚)

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👑 OPTIONS 👑

💖 Options to specify input files:

• -f [<.xvg>] (graph.xvg) — xvgr/xmgr file
• -ge [<.xvg>] (gibbs.xvg) (Optional) — xvgr/xmgr file
• -ene [<.xvg>] (esham.xvg) (Optional) — xvgr/xmgr file

🎀 Options to specify output files:

• -dist [<.xvg>] (ener.xvg) (Optional) — xvgr/xmgr file
• -histo [<.xvg>] (edist.xvg) (Optional) — xvgr/xmgr file
• -bin [<.ndx>] (bindex.ndx) (Optional) — Index file
• -lp [<.xpm>] (prob.xpm) (Optional) — X PixMap compatible matrix file
• -ls [<.xpm>] (gibbs.xpm) (Optional) — X PixMap compatible matrix file
• -lsh [<.xpm>] (enthalpy.xpm) (Optional) — X PixMap compatible matrix file
• -lss [<.xpm>] (entropy.xpm) (Optional) — X PixMap compatible matrix file
• -ls3 [<.pdb>] (gibbs3.pdb) (Optional) — Protein data bank file
• -g [<.log>] (shamlog.log) (Optional) — Log file

🌈 Other options:

• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files. like, auto-open them for you? cute.
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none. pick your aesthetic bestie ✨
• -[no]time (yes) — Expect a time in the input
• -b <real> (-1) — First time to read from set
• -e <real> (-1) — Last time to read from set
• -ttol <real> (0) — Tolerance on time in appropriate units (usually ps)
• -n <int> (1) — Read this number of sets separated by lines containing only an ampersand. the &-separated sets thing 🫶
• -[no]d (no) — Use the derivative
• -[no]sham (yes) — Turn off energy weighting even if energies are given
• -tsham <real> (298.15) — Temperature for single histogram analysis
• -pmin <real> (0) — Minimum probability. Anything lower than this will be set to zero. 🚫
• -dim <vector> (1 1 1) — Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)
• -ngrid <vector> (32 32 32) — Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)
• -xmin <vector> (0 0 0) — Minimum for the axes in energy landscape (see above for > 3 dimensions)
• -xmax <vector> (1 1 1) — Maximum for the axes in energy landscape (see above for > 3 dimensions)
• -pmax <real> (0) — Maximum probability in output, default is calculate
• -gmax <real> (0) — Maximum free energy in output, default is calculate
• -emin <real> (0) — Minimum enthalpy in output, default is calculate
• -emax <real> (0) — Maximum enthalpy in output, default is calculate
• -nlevels <int> (25) — Number of levels for energy landscape

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🦋 SEE ALSO 🦋

• gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>. go click it, fr fr 💜

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💜 COPYRIGHT 💜

2026, GROMACS development team

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okay that's the whole thing, no notes, you're so ready to sham 🧚✨ and hey — this was GROMACS 2026.4, dated Oct 02, 2026. slay, go make some free energy landscapes bestie 💅🎀👑