GMX-DSSP(1)

💖 GMX-DSSP 💖

okay bestie, welcome to the GROMACS manual page for gmx-dssp — yes it's a real page in the GROMACS manual, section 1, and yes we're gonna get through it together 🫶

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✨ NAME ✨

gmx-dssp — calculate protein secondary structure via DSSP algorithm 🧬💅

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🌸 SYNOPSIS 🌸

gmx dssp [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-o [<.dat>]] [-num [<.xvg>]] [-b <time>] [-e <time>]
         [-dt <time>] [-tu <enum>] [-fgroup <selection>]
         [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
         [-selrpos <enum>] [-seltype <enum>] [-sel <selection>]
         [-hmode <enum>] [-hbond <enum>] [-[no]nb] [-cutoff <real>]
         [-[no]clear] [-[no]pihelix] [-ppstretch <enum>]
         [-[no]polypro]

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🦋 DESCRIPTION 🦋

so gmx dssp lets you use the DSSP algorithm — and like, specifically the way it detects particular patterns of hydrogen bonds between amino acid residues — to figure out the secondary structure of a protein. it's giving structural biology main character energy fr fr 💜

here are the one-symbol secondary structure designations that show up in the output file, and you're gonna want to know all of them:

• H — alpha-helix;
• B — residue in isolated beta-bridge;
• E — extended strand that participates in beta-ladder;
• G — 3_10-helix;
• I — pi-helix;
• P — kappa-helix (poly-proline II helix);
• S — bend;
• T — hydrogen-bonded turn;
• = — break;
• ~ — loop (no special secondary structure designation).

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-num is your bestie for getting a plot of the number of secondary structures of each type as a function of time at the output 📈✨

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-hmode selects between using hydrogen atoms directly from the structure (that's the "gromacs" option) and using hydrogen pseudo-atoms based on C and O atom coordinates of previous residue (that's the "dssp" option). and listen — you should always use the "dssp" option for structures with absent hydrogen atoms! no cap 🙈

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-hbond selects between different definitions of hydrogen bond. "energy" means the calculation of a hydrogen bond using the electrostatic interaction energy, and "geometry" means the calculation of the hydrogen bond using geometric criterion for the existence of a hydrogen bond ⚡

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-nb allows using the GROMACS neighbor-search method to find residue pairs that may have a hydrogen bond, instead of simply iterating over the residues among themselves. lowkey a whole different vibe 👑

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-cutoff is a real value that defines maximum distance from residue to its neighbor residue used in -nb. minimum (and also recommended) value is 0.9. periodt 🎀

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-clear allows you to ignore the analysis of the secondary structure residues that are missing one or more critical atoms (CA, C, N, O or H). always use this option together with -hmode dssp for structures that lack hydrogen atoms! 🫶

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-pihelix changes pattern-search algorithm towards preference of pi-helices 🌀

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-ppstretch defines stretch value of polyproline-helices. "shortened" means stretch with size 2 and "default" means stretch with size 3.

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-polypro enables the search for polyproline helices (default behavior, equivalent to DSSP v4). disabling this option will result in disabling the search for polyproline helices, reproducing the behavior of DSSP v2 🌈

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⚠️ okay important one: note that gmx dssp currently is not capable of reproducing the secondary structure of proteins whose structure is determined by methods other than X-ray crystallography (structures in .pdb format with incorrect values in the CRYST1 line) due to the incorrect cell size in such structures. it's not her fault, it's the cell size's fault 💀

⚠️ also please note that the computation is always done in single precision, regardless of the precision for which GROMACS was configured. single precision only, no exceptions, iykyk 😭

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✨ OPTIONS ✨

🎀 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — input structure: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) (Optional) — extra index groups

🧚 Options to specify output files:

• -o [<.dat>] (dssp.dat) — filename for DSSP output
• -num [<.xvg>] (num.xvg) (Optional) — output file name for secondary structures statistics for the trajectory

👑 Other options:

• -b <time> (0) — first frame (ps) to read from trajectory
• -e <time> (0) — last frame (ps) to read from trajectory
• -dt <time> (0) — only use frame if t MOD dt == first time (ps)
• -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: 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
• -seltype <enum> (atom) — default selection output positions: 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
• -sel <selection> — group for DSSP
• -hmode <enum> (gromacs) — hydrogens pseudoatoms creating mode: gromacs, dssp
• -hbond <enum> (energy) — selects between different definitions of hydrogen bond: energy, geometry
• -[no]nb (yes) — use GROMACS neighbor-search method
• -cutoff <real> (0.9) — distance from residue to its neighbor residue in neighbor search. must be >= 0.9
• -[no]clear (no) — clear defective residues from the structure
• -[no]pihelix (no) — prefer Pi Helices
• -ppstretch <enum> (default) — stretch value for PP-helices: shortened, default
• -[no]polypro (yes) — perform a search for polyproline helices

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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 that 💅✨ this was GMX-DSSP(1) from the GROMACS manual, version 2026.4, dated Oct 02, 2026 — go calculate some secondary structure, you absolute icon 👑🎀