Command reference
openmm-cli
OpenMM command line interface.
Usage:
console
$ openmm-cli [OPTIONS] COMMAND [ARGS]...
Options:
--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.
Commands:
dashboard: Launch a web dashboard that plots CSV...run: Run an MD simulation from a YAML config file.prepare: System preparation commands.trajectory: Trajectory analysis and processing.
openmm-cli dashboard
Launch a web dashboard that plots CSV output files
Usage:
console
$ openmm-cli dashboard [OPTIONS] [DIRECTORY]
Arguments:
[DIRECTORY]: Directory to display. Defaults to the current directory. [default: .]
Options:
--port INTEGER: Port to serve on. [default: 8501]--help: Show this message and exit.
openmm-cli run
Run an MD simulation from a YAML config file.
Usage:
console
$ openmm-cli run [OPTIONS] CONFIG
Arguments:
CONFIG: Path to yaml configuration file. [required]
Options:
--help: Show this message and exit.
openmm-cli prepare
System preparation commands.
Usage:
console
$ openmm-cli prepare [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
clean: Clean a PDB file with pdbfixer: fix...solvate: Add a water box and counterions to bring...
openmm-cli prepare clean
Clean a PDB file with pdbfixer: fix structure, add hydrogens, optionally strip extras.
Usage:
console
$ openmm-cli prepare clean [OPTIONS] PDB
Arguments:
PDB: Input PDB file. [required]
Options:
--out PATH: Output PDB file. [default: cleaned.pdb]--ph FLOAT: pH used to assign protonation states. [default: 7.4]--keep-water / --strip-water: Keep crystallographic water molecules (only applies when stripping heteroatoms). [default: strip-water]--keep-hetero / --strip-hetero: Keep ligands, cofactors, and ions. Off by default for protein-only output. [default: strip-hetero]--add-residues / --no-add-residues: Build in missing residues (gaps/loops). Off by default to avoid silent insertions. [default: no-add-residues]--replace-nonstandard / --keep-nonstandard: Replace nonstandard residues (e.g. MSE -> MET) with their standard equivalents. [default: replace-nonstandard]--help: Show this message and exit.
openmm-cli prepare solvate
Add a water box and counterions to bring the system to the target ionic strength.
Usage:
console
$ openmm-cli prepare solvate [OPTIONS] PDB
Arguments:
PDB: Input PDB file (typically already cleaned). [required]
Options:
--out PATH: Output solvated PDB file. [default: solvated.pdb]--padding FLOAT: Minimum distance (nm) from solute to box edge. [default: 1.0]--box-shape [cube|dodecahedron|octahedron]: Shape of the periodic box. [default: cube]--ionic-strength FLOAT: Ionic strength in mol/L (physiological ~0.15). [default: 0.15]--positive-ion TEXT: Cation species (Na+, K+, Li+, Rb+, Cs+). [default: Na+]--negative-ion TEXT: Anion species (Cl-, Br-, F-, I-). [default: Cl-]--help: Show this message and exit.
openmm-cli trajectory
Trajectory analysis and processing.
Usage:
console
$ openmm-cli trajectory [OPTIONS] COMMAND [ARGS]...
Options:
--help: Show this message and exit.
Commands:
align: Align each frame to a reference by RMSD...angle: Angle A-B-C over time, using the center of...average: Average a trajectory's coordinates into a...center: Translate each frame so the selection's...convert: Convert a trajectory between formats.dihedral: Dihedral angle A-B-C-D over time, using...distance: Distance (nm) between two atom selections...extract: Extract a frame range ...hbonds: List hydrogen bonds present in at least...image: Image molecules into the primary unit...info: Print frames, atoms, residues, chains, and...rmsd: RMSD (nm) of each frame versus a...rmsf: Per-atom RMSF (nm) of the selected atoms...strip: Keep only the selected atoms; write a...
openmm-cli trajectory align
Align each frame to a reference by RMSD fit on the selected atoms.
Usage:
console
$ openmm-cli trajectory align [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: Input trajectory file. [required]
Options:
--top PATH: Topology file (parm7, pdb, ...). [required]--out PATH: Output trajectory. [default: aligned.dcd]--ref PATH: Reference structure (default: first frame of trajectory).--sel TEXT: Atoms to use for the fit (mdtraj selection syntax). [default: name CA]--help: Show this message and exit.
openmm-cli trajectory angle
Angle A-B-C over time, using the center of mass of each selection (B is the vertex).
Usage:
console
$ openmm-cli trajectory angle [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--a TEXT: First selection. [required]--b TEXT: Second selection (the vertex). [required]--c TEXT: Third selection. [required]--out PATH: [default: angle.csv]--degrees / --radians: [default: degrees]--help: Show this message and exit.
openmm-cli trajectory average
Average a trajectory's coordinates into a single structure.
Usage:
console
$ openmm-cli trajectory average [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: Input trajectory. [required]
Options:
--top PATH: Topology file. [required]--sel TEXT: Atoms to superpose on before averaging. [default: name CA]--out PATH: Output structure file (format by extension). [default: average.pdb]--iterations INTEGER: Re-superpose onto the running average N times. [default: 2]--help: Show this message and exit.
openmm-cli trajectory center
Translate each frame so the selection's COM sits at the target, then by default image molecules.
Usage:
console
$ openmm-cli trajectory center [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: centered.dcd]--sel TEXT: Selection whose center of mass should be moved. [default: protein]--target [box|origin]: Where to place the COM. [default: box]--image / --no-image: Image molecules into the unit cell after centering. [default: image]--help: Show this message and exit.
openmm-cli trajectory convert
Convert a trajectory between formats. Output format is inferred from the extension.
Usage:
console
$ openmm-cli trajectory convert [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: Input trajectory. [required]
Options:
--top PATH: [required]--out PATH: Output trajectory; format inferred from extension (.dcd, .xtc, .trr, .nc, .h5). [default: converted.xtc]--help: Show this message and exit.
openmm-cli trajectory dihedral
Dihedral angle A-B-C-D over time, using the center of mass of each selection.
Usage:
console
$ openmm-cli trajectory dihedral [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--a TEXT: [required]--b TEXT: [required]--c TEXT: [required]--d TEXT: [required]--out PATH: [default: dihedral.csv]--degrees / --radians: [default: degrees]--help: Show this message and exit.
openmm-cli trajectory distance
Distance (nm) between two atom selections over time.
Usage:
console
$ openmm-cli trajectory distance [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--a TEXT: First atom selection. [required]--b TEXT: Second atom selection. [required]--out PATH: [default: distance.csv]--help: Show this message and exit.
openmm-cli trajectory extract
Extract a frame range from a trajectory.
Usage:
console
$ openmm-cli trajectory extract [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: extracted.dcd]--start INTEGER: First frame (0-indexed). [default: 0]--stop INTEGER: Stop frame (exclusive). Default: end.--stride INTEGER: Take every Nth frame. [default: 1]--help: Show this message and exit.
openmm-cli trajectory hbonds
List hydrogen bonds present in at least freq of frames, with their per-bond occupancy.
Usage:
console
$ openmm-cli trajectory hbonds [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: hbonds.csv]--freq FLOAT: Minimum fraction of frames an H-bond must be present (0-1). [default: 0.1]--sel TEXT: Restrict to H-bonds where both donor and acceptor are in this selection.--help: Show this message and exit.
openmm-cli trajectory image
Image molecules into the primary unit cell, keeping them whole across boundaries.
Usage:
console
$ openmm-cli trajectory image [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: imaged.dcd]--help: Show this message and exit.
openmm-cli trajectory info
Print frames, atoms, residues, chains, and box information.
Usage:
console
$ openmm-cli trajectory info [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--help: Show this message and exit.
openmm-cli trajectory rmsd
RMSD (nm) of each frame versus a reference, after optimal alignment.
Usage:
console
$ openmm-cli trajectory rmsd [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: rmsd.csv]--ref PATH: Reference structure (default: first frame).--sel TEXT: Atoms for the fit and RMSD calculation. [default: name CA]--help: Show this message and exit.
openmm-cli trajectory rmsf
Per-atom RMSF (nm) of the selected atoms over the trajectory.
Usage:
console
$ openmm-cli trajectory rmsf [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: rmsf.csv]--sel TEXT: [default: name CA]--align / --no-align: RMSD-fit trajectory to frame 0 before computing RMSF. [default: align]--help: Show this message and exit.
openmm-cli trajectory strip
Keep only the selected atoms; write a stripped trajectory and matching topology.
Usage:
console
$ openmm-cli trajectory strip [OPTIONS] TRAJECTORY
Arguments:
TRAJECTORY: [required]
Options:
--top PATH: [required]--out PATH: [default: stripped.dcd]--keep TEXT: Atoms to keep (mdtraj selection). [default: not water]--top-out PATH: Where to write the stripped topology (PDB). [default: stripped.pdb]--help: Show this message and exit.