GMX-DISRE(1)

✨ GMX-DISRE(1) ✨ — like, the GROMACS manual page for gmx-disre, bestie 💖

okay so you opened the GROMACS manpage for gmx-disre and honestly? iconic behavior. let's get into it 👑

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🌸 NAME 🌸

gmx-disre — bestie, it analyzes distance restraints. that's the whole vibe. distance restraints. analyzed. slay.

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🦋 SYNOPSIS 🦋

gmx disre [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
          [-c [<.ndx>]] [-ds [<.xvg>]] [-da [<.xvg>]] [-dn [<.xvg>]]
          [-dm [<.xvg>]] [-dr [<.xvg>]] [-l [<.log>]] [-q [<.pdb>]]
          [-x [<.xpm>]] [-b <time>] [-e <time>] [-dt <time>] [-[no]w]
          [-xvg <enum>] [-ntop <int>] [-maxdr <real>]
          [-nlevels <int>] [-[no]third]

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💅 DESCRIPTION 💅

so gmx disre computes violations of distance restraints. that's its whole job, and it does it well, periodt.

the program always computes the instantaneous violations rather than time-averaged ones — like, no cap. why? because this analysis happens on a trajectory file afterwards, so time averaging genuinely does not make sense here. but — and this is the cute part — the time averaged values per restraint do get written into the log file. so you're not missing out 🫶

an index file may be used to select specific restraints by index group label, purely for printing purposes. fancy ✨

when the optional -q flag is given, you get a .pdb file coloured by the amount of average violations. cute, visual, obsessed.

when the -c option is given, an index file gets read containing the frames in your trajectory that correspond to the clusters (which are defined some other way, not by this program, iykyk) that you want to analyze. for these clusters the program will compute average violations using the third power averaging algorithm and print them in the log file. math ✨

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🎀 OPTIONS 🎀

💜 Options to specify input files:

• -s [<.tpr>] (topol.tpr) — Portable xdr run input file. the whole starting point, fr fr
• -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng h5md. so many formats, she's versatile 💅
• -n [<.ndx>] (viol.ndx) (Optional) — Index file
• -c [<.ndx>] (clust.ndx) (Optional) — Index file. yes there are two index files, they do different things, don't @ me

🩷 Options to specify output files:

• -ds [<.xvg>] (drsum.xvg) — xvgr/xmgr file
• -da [<.xvg>] (draver.xvg) — xvgr/xmgr file
• -dn [<.xvg>] (drnum.xvg) — xvgr/xmgr file
• -dm [<.xvg>] (drmax.xvg) — xvgr/xmgr file
• -dr [<.xvg>] (restr.xvg) — xvgr/xmgr file
• -l [<.log>] (disres.log) — Log file
• -q [<.pdb>] (viol.pdb) (Optional) — Protein data bank file
• -x [<.xpm>] (matrix.xpm) (Optional) — X PixMap compatible matrix file

🌈 Other options:

• -b <time> (0) — Time of first frame to read from trajectory (default unit ps)
• -e <time> (0) — Time of last frame to read from trajectory (default unit ps)
• -dt <time> (0) — Only use frame when t MOD dt = first time (default unit ps)
• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -ntop <int> (0) — Number of large violations that are stored in the log file every step
• -maxdr <real> (0) — Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.
• -nlevels <int> (20) — Number of levels in the matrix output
• -[no]third (yes) — Use inverse third power averaging or linear for matrix output

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🔥 SEE ALSO 🔥

• gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

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👑 COPYRIGHT 👑

2026, GROMACS development team

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and that's the whole thing, bestie 🫶 go analyze those restraints, you absolute main character. this was GROMACS 2026.4, dated Oct 02, 2026 — so yes she's recent, so yes she's relevant 💖 periodt. ✨