GMX-CONVERT-TRJ(1)

✨ NAME ✨

okay so this is gmx-convert-trj, from the GROMACS manual (section 1, bestie) — and it does exactly what it says on the tin: it converts between different trajectory types. 💅

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🦋 SYNOPSIS 🦋

gmx convert-trj [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
             [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-b <time>]
             [-e <time>] [-dt <time>] [-tu <enum>]
             [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
             [-[no]pbc] [-sf <file>] [-selrpos <enum>]
             [-select <selection>] [-vel <enum>] [-force <enum>]
             [-atoms <enum>] [-precision <int>] [-starttime <time>]
             [-timestep <time>] [-box <vector>]

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💖 DESCRIPTION 💖

so like. gmx convert-trj converts trajectory files between different formats. it literally writes every GROMACS-supported file format from the supported input formats. no cap, all of them. 🔥

it also comes with a lil selection of options to modify individual trajectory frames, including options to produce slimmer output files (yes queen, smaller trajectories). and you can also straight-up replace the particle information stored in the input trajectory with the ones from a structure file. it's giving glow-up but for atoms. ✨

the module can also generate subsets of trajectories based on selections you supply. so you're the main character picking and choosing what stays. 👑

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🌸 OPTIONS 🌸

🎀 Options to specify input files

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — input trajectory or single configuration. she accepts: xtc trr cpt gro g96 pdb tng h5md 🦋
• -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — input structure. she accepts: tpr gro g96 pdb brk ent 🌸
• -n [<.ndx>] (index.ndx) (Optional) — extra index groups, if you've got some 💜

💅 Options to specify output files

• -o [<.xtc/.trr/...>] (trajout.xtc) — output trajectory. options are: xtc trr cpt gro g96 pdb tng h5md ✨

🧚 Other options

• -b <time> (0) — first frame (ps) to read from the trajectory 🕐
• -e <time> (0) — last frame (ps) to read from the trajectory 🕐
• -dt <time> (0) — only use a frame if t MOD dt == first time (ps). fr fr, that's the condition 💀
• -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s ⏳
• -fgroup <selection> — atoms stored in the trajectory file (if not set, assume first N atoms) 🙈
• -xvg <enum> (xmgrace) — plot formatting: xmgrace, xmgr, none 🎨
• -[no]rmpbc (yes) — make molecules whole for each frame 🫶
• -[no]pbc (yes) — use periodic boundary conditions for distance calculation 🌈
• -sf <file> — provide selections from files 📂
• -selrpos <enum> (atom) — selection reference positions, and babes there are a LOT: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog 👑
• -select <selection> — selection of particles to write to the file ✍️
• -vel <enum> (preserved-if-present) — save velocities from the frame if possible: preserved-if-present, always, never 💨
• -force <enum> (preserved-if-present) — save forces from the frame if possible: preserved-if-present, always, never 💪
• -atoms <enum> (preserved-if-present) — decide on providing new atom information from topology vs using the current frame atom information: preserved-if-present, always-from-structure, never, always 🧬
• -precision <int> (3) — set output precision to a custom value 🔍
• -starttime <time> (0) — change start time for the first frame ⏰
• -timestep <time> (0) — change the time between different frames ⏱️
• -box <vector> — new diagonal box vector for the output frame 📦

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🔥 SEE ALSO 🔥

• gmx(1)

more info about GROMACS is available at <http://www.gromacs.org/>. go look, bestie, it's iconic 🌐

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💜 COPYRIGHT 💜

2026, GROMACS development team

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and that's the whole vibe check 🫶 this page is GROMACS 2026.4, dated Oct 02, 2026 — so if you're reading this in the future, hiii, you're a time traveler, slay 💅✨