GMX-VANHOVE(1)

✨ gmx-vanhove ✨

okay bestie, gather round, because this is the GROMACS manual page for gmx-vanhove and she is serving physics 💖 the vibe? computing Van Hove displacement and correlation functions. no cap.

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🦋 SYNOPSIS 🦋

gmx vanhove [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-om [<.xpm>]] [-or [<.xvg>]] [-ot [<.xvg>]] [-b <time>]
            [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
            [-sqrt <real>] [-fm <int>] [-rmax <real>] [-rbin <real>]
            [-mmax <real>] [-nlevels <int>] [-nr <int>] [-fr <int>]
            [-rt <real>] [-ft <int>]

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🌸 DESCRIPTION 🌸

so gmx vanhove computes the Van Hove correlation function. and like, what even is that? the Van Hove G(r,t) is the probability that a particle that is at r_0 at time zero can be found at position r_0+r at time t. periodt. but gmx vanhove is a lil different — it determines G not for a vector r, but for the length of r. so basically it gives you the probability that a particle moves a distance of r in time t. cute right?

jumps across the periodic boundaries? removed. gone. not invited. 🙈 and corrections are made for scaling due to isotropic or anisotropic pressure coupling. she's thorough.

• with option -om the whole matrix can be written as a function of t and r, or as a function of sqrt(t) and r (that's the -sqrt option, iykyk).
• with option -or the Van Hove function is plotted for one or more values of t. -nr sets the number of times, -fr the number spacing between the times. the binwidth is set with -rbin. the number of bins is determined automatically ✨
• with option -ot the integral up to a certain distance (that's -rt) is plotted as a function of time.

⚠️ okay important, bestie: for all frames that are read, the coordinates of the selected particles are stored in memory. so this program may use a lot of memory 😭. and for options -om and -ot the program may be slow. why? because the calculation scales as the number of frames times -fm or -ft. but!!! note that with the -dt option the memory usage and calculation time can be reduced. slay. 💅

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💅 OPTIONS 💅

🎀 Options to specify input files: 🎀

• -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory, bestie. formats: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) — structure + mass(db). formats: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) — index file. (optional, no pressure)

🌈 Options to specify output files: 🌈

• -om [<.xpm>] (vanhove.xpm) — an X PixMap compatible matrix file. iconic. (optional)
• -or [<.xvg>] (vanhove_r.xvg) — an xvgr/xmgr file. (optional)
• -ot [<.xvg>] (vanhove_t.xvg) — an xvgr/xmgr file. (optional)

⭐ Other options: ⭐

• -b <time> (0) — time of first frame to read from trajectory (default unit is ps)
• -e <time> (0) — time of last frame to read from trajectory (default unit is ps)
• -dt <time> (0) — only use frame when t MOD dt = first time (default unit is ps)
• -[no]w (no) — view output .xvg, .xpm, .eps and .pdb files
• -xvg <enum> (xmgrace) — xvg plot formatting. your choices: xmgrace, xmgr, none
• -sqrt <real> (0) — use sqrt(t) on the matrix axis, which is binspacing # in sqrt(ps)
• -fm <int> (0) — number of frames in the matrix, 0 is plot all
• -rmax <real> (2) — maximum r in the matrix (nm)
• -rbin <real> (0.01) — binwidth in the matrix and for -or (nm)
• -mmax <real> (0) — maximum density in the matrix, 0 is calculate (1/nm)
• -nlevels <int> (81) — number of levels in the matrix
• -nr <int> (1) — number of curves for the -or output
• -fr <int> (0) — frame spacing for the -or output
• -rt <real> (0) — integration limit for the -ot output (nm)
• -ft <int> (0) — number of frames in the -ot output, 0 is plot all

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🫶 SEE ALSO 🫶

• gmx(1)

more info about GROMACS is available at <http://www.gromacs.org/>. go read it, bestie, it's giving knowledge 💜

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👑 COPYRIGHT 👑

2026, GROMACS development team

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and that's the whole page, mwah 💋 this was 2026.4, dated Oct 02, 2026, brought to you by the GROMACS girlies — GMX-VANHOVE(1), periodt. 🎀✨