# Package gromacs-common

GROMACS shared data and documentation

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for bio-molecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package includes architecture independent data and HTML documentation.

Version: 2024.3

## General Commands | |

gmx | molecular dynamics simulation suite |

gmx-anaeig | Analyze eigenvectors/normal modes |

gmx-analyze | Analyze data sets |

gmx-angle | Calculate distributions and correlations for angles and dihedrals |

gmx-awh | Extract data from an accelerated weight histogram (AWH) run |

gmx-bar | Calculate free energy difference estimates through Bennett's acceptance ratio |

gmx-bundle | Analyze bundles of axes, e.g., helices |

gmx-check | Check and compare files |

gmx-chi | Calculate everything you want to know about chi and other dihedrals |

gmx-cluster | Cluster structures |

gmx-clustsize | Calculate size distributions of atomic clusters |

gmx-confrms | Fit two structures and calculates the RMSD |

gmx-convert-tpr | Make a modified run-input file |

gmx-convert-trj | Converts between different trajectory types |

gmx-covar | Calculate and diagonalize the covariance matrix |

gmx-current | Calculate dielectric constants and current autocorrelation function |

gmx-density | Calculate the density of the system |

gmx-densmap | Calculate 2D planar or axial-radial density maps |

gmx-densorder | Calculate surface fluctuations |

gmx-dielectric | Calculate frequency dependent dielectric constants |

gmx-dipoles | Compute the total dipole plus fluctuations |

gmx-disre | Analyze distance restraints |

gmx-distance | Calculate distances between pairs of positions |

gmx-dos | Analyze density of states and properties based on that |

gmx-dssp | Calculate protein secondary structure via DSSP algorithm |

gmx-dump | Make binary files human readable |

gmx-dyecoupl | Extract dye dynamics from trajectories |

gmx-editconf | Convert and manipulates structure files |

gmx-eneconv | Convert energy files |

gmx-enemat | Extract an energy matrix from an energy file |

gmx-energy | Writes energies to xvg files and display averages |

gmx-extract-cluster | Allows extracting frames corresponding to clusters from trajectory |

gmx-filter | Frequency filter trajectories, useful for making smooth movies |

gmx-freevolume | Calculate free volume |

gmx-gangle | Calculate angles |

gmx-genconf | Multiply a conformation in 'random' orientations |

gmx-genion | Generate monoatomic ions on energetically favorable positions |

gmx-genrestr | Generate position restraints or distance restraints for index groups |

gmx-grompp | Make a run input file |

gmx-gyrate | Calculate radius of gyration of a molecule |

gmx-gyrate-legacy | Calculate the radius of gyration |

gmx-h2order | Compute the orientation of water molecules |

gmx-hbond | Compute and analyze hydrogen bonds. |

gmx-hbond-legacy | Compute and analyze hydrogen bonds |

gmx-helix | Calculate basic properties of alpha helices |

gmx-helixorient | Calculate local pitch/bending/rotation/orientation inside helices |

gmx-help | Print help information |

gmx-hydorder | Compute tetrahedrality parameters around a given atom |

gmx-insert-molecules | Insert molecules into existing vacancies |

gmx-lie | Estimate free energy from linear combinations |

gmx-make_edi | Generate input files for essential dynamics sampling |

gmx-make_ndx | Make index files |

gmx-mdmat | Calculate residue contact maps |

gmx-mdrun | Perform a simulation, do a normal mode analysis or an energy minimization |

gmx-mindist | Calculate the minimum distance between two groups |

gmx-mk_angndx | Generate index files for 'gmx angle' |

gmx-msd | Compute mean squared displacements |

gmx-nmeig | Diagonalize the Hessian for normal mode analysis |

gmx-nmens | Generate an ensemble of structures from the normal modes |

gmx-nmr | Analyze nuclear magnetic resonance properties from an energy file |

gmx-nmtraj | Generate a virtual oscillating trajectory from an eigenvector |

gmx-nonbonded-benchmark | Benchmarking tool for the non-bonded pair kernels. |

gmx-order | Compute the order parameter per atom for carbon tails |

gmx-pairdist | Calculate pairwise distances between groups of positions |

gmx-pdb2gmx | Convert coordinate files to topology and FF-compliant coordinate files |

gmx-pme_error | Estimate the error of using PME with a given input file |

gmx-polystat | Calculate static properties of polymers |

gmx-potential | Calculate the electrostatic potential across the box |

gmx-principal | Calculate principal axes of inertia for a group of atoms |

gmx-rama | Compute Ramachandran plots |

gmx-rdf | Calculate radial distribution functions |

gmx-report-methods | Write short summary about the simulation setup to a text file and/or to the standard output. |

gmx-rms | Calculate RMSDs with a reference structure and RMSD matrices |

gmx-rmsdist | Calculate atom pair distances averaged with power -2, -3 or -6 |

gmx-rmsf | Calculate atomic fluctuations |

gmx-rotacf | Calculate the rotational correlation function for molecules |

gmx-rotmat | Plot the rotation matrix for fitting to a reference structure |

gmx-saltbr | Compute salt bridges |

gmx-sans-legacy | Compute small angle neutron scattering spectra |

gmx-sasa | Compute solvent accessible surface area |

gmx-saxs-legacy | Compute small angle X-ray scattering spectra |

gmx-scattering | Calculate small angle scattering profiles for SANS or SAXS |

gmx-select | Print general information about selections |

gmx-sham | Compute free energies or other histograms from histograms |

gmx-sigeps | Convert c6/12 or c6/cn combinations to and from sigma/epsilon |

gmx-solvate | Solvate a system |

gmx-sorient | Analyze solvent orientation around solutes |

gmx-spatial | Calculate the spatial distribution function |

gmx-spol | Analyze solvent dipole orientation and polarization around solutes |

gmx-tcaf | Calculate viscosities of liquids |

gmx-traj | Plot x, v, f, box, temperature and rotational energy from trajectories |

gmx-trajectory | Print coordinates, velocities, and/or forces for selections |

gmx-trjcat | Concatenate trajectory files |

gmx-trjconv | Convert and manipulates trajectory files |

gmx-trjorder | Order molecules according to their distance to a group |

gmx-tune_pme | Time mdrun as a function of PME ranks to optimize settings |

gmx-vanhove | Compute Van Hove displacement and correlation functions |

gmx-velacc | Calculate velocity autocorrelation functions |

gmx-wham | Perform weighted histogram analysis after umbrella sampling |

gmx-wheel | Plot helical wheels |

gmx-x2top | Generate a primitive topology from coordinates |

gmx-xpm2ps | Convert XPM (XPixelMap) matrices to postscript or XPM |