GMX-CLUSTSIZE(1)

💅 GMX-CLUSTSIZE(1) 💅

okay bestie, welcome to the GROMACS manual page for gmx-clustsize — literally the girl who counts your atoms' little friendship circles 💖

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✨ NAME ✨

gmx-clustsize — Calculate size distributions of atomic clusters 🫶

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✨ SYNOPSIS ✨

gmx clustsize [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]]
             [-o [<.xpm>]] [-ow [<.xpm>]] [-nc [<.xvg>]]
             [-mc [<.xvg>]] [-ac [<.xvg>]] [-hc [<.xvg>]]
             [-temp [<.xvg>]] [-mcn [<.ndx>]] [-b <time>] [-e <time>]
             [-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
             [-cut <real>] [-[no]mol] [-[no]pbc] [-nskip <int>]
             [-nlevels <int>] [-ndf <int>] [-rgblo <vector>]
             [-rgbhi <vector>]

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🌸 DESCRIPTION 🌸

so gmx clustsize computes the size distributions of molecular/atomic clusters in the gas phase. it's giving who's clumped with who energy. the output comes at you as an .xpm file, and the total number of clusters gets written into an .xvg file. two files, one iconic task ✨

when you pass the -mol option, clusters get made out of molecules instead of atoms, which is what lets you cluster big molecules (glow-up fr). but heads up bestie — in that case an index file would still contain atom numbers, or your calculation will die with a SEGV 😭💀 no cap, it will just perish.

when velocities are present in your trajectory, the temperature of the largest cluster gets printed in a separate .xvg file, assuming the particles are free to move 🦋 if you're using constraints, please correct the temperature yourself. for instance, water simulated with SHAKE or SETTLE will yield a temperature that is 1.5 times too low 😳 you can compensate for this with the -ndf option. and remember to take the removal of center of mass motion into account, okay? don't forget, that's the whole vibe check 🎀

the -mc option will produce an index file containing the atom numbers of the largest cluster 👑

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💅 OPTIONS 💅

🍓 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr>] (topol.tpr) (Optional) — Portable xdr run input file
• -n [<.ndx>] (index.ndx) (Optional) — Index file

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🎀 Options to specify output files:

• -o [<.xpm>] (csize.xpm) — X PixMap compatible matrix file
• -ow [<.xpm>] (csizew.xpm) — X PixMap compatible matrix file
• -nc [<.xvg>] (nclust.xvg) — xvgr/xmgr file
• -mc [<.xvg>] (maxclust.xvg) — xvgr/xmgr file
• -ac [<.xvg>] (avclust.xvg) — xvgr/xmgr file
• -hc [<.xvg>] (histo-clust.xvg) — xvgr/xmgr file
• -temp [<.xvg>] (temp.xvg) (Optional) — xvgr/xmgr file
• -mcn [<.ndx>] (maxclust.ndx) (Optional) — Index file

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🌈 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)
• -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s
• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -cut <real> (0.35) — Largest distance (nm) to be considered in a cluster
• -[no]mol (no) — Cluster molecules rather than atoms (needs .tpr file)
• -[no]pbc (yes) — Use periodic boundary conditions
• -nskip <int> (0) — Number of frames to skip between writing
• -nlevels <int> (20) — Number of levels of grey in .xpm output
• -ndf <int> (-1) — Number of degrees of freedom of the entire system for temperature calculation. If not set, the number of atoms times three is used.
• -rgblo <vector> (1 1 0) — RGB values for the color of the lowest occupied cluster size
• -rgbhi <vector> (0 0 1) — RGB values for the color of the highest occupied cluster size

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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 page bestie, you ate 💅✨ this queen lives in the GROMACS 2026.4 manual, dated Oct 02, 2026 — go forth and cluster, you've got this 🫶💖🌸