# Manual pages

Origin: 2018.1.

[ Alias ↣ ] Name (section) | Brief |
---|---|

gmx(1) | Molecular dynamics simulation suite. |

gmx-anadock(1) | Cluster structures from Autodock runs. |

gmx-anaeig(1) | Analyze eigenvectors/normal modes. |

gmx-analyze(1) | Analyze data sets. |

gmx-angle(1) | Calculate distributions and correlations for angles and dihedrals. |

gmx-awh(1) | Extract data from an accelerated weight histogram (AWH) run. |

gmx-bar(1) | Calculate free energy difference estimates through Bennett's acceptance ratio. |

gmx-bundle(1) | Analyze bundles of axes, e.g., helices. |

gmx-check(1) | Check and compare files. |

gmx-chi(1) | Calculate everything you want to know about chi and other dihedrals. |

gmx-cluster(1) | Cluster structures. |

gmx-clustsize(1) | Calculate size distributions of atomic clusters. |

gmx-confrms(1) | Fit two structures and calculates the RMSD. |

gmx-convert-tpr(1) | Make a modifed run-input file. |

gmx-covar(1) | Calculate and diagonalize the covariance matrix. |

gmx-current(1) | Calculate dielectric constants and current autocorrelation function. |

gmx-density(1) | Calculate the density of the system. |

gmx-densmap(1) | Calculate 2D planar or axial-radial density maps. |

gmx-densorder(1) | Calculate surface fluctuations. |

gmx-dielectric(1) | Calculate frequency dependent dielectric constants. |

gmx-dipoles(1) | Compute the total dipole plus fluctuations. |

gmx-disre(1) | Analyze distance restraints. |

gmx-distance(1) | Calculate distances between pairs of positions. |

gmx-do_dssp(1) | Assign secondary structure and calculate solvent accessible surface area. |

gmx-dos(1) | Analyze density of states and properties based on that. |

gmx-dump(1) | Make binary files human readable. |

gmx-dyecoupl(1) | Extract dye dynamics from trajectories. |

gmx-dyndom(1) | Interpolate and extrapolate structure rotations. |

gmx-editconf(1) | Convert and manipulates structure files. |

gmx-eneconv(1) | Convert energy files. |

gmx-enemat(1) | Extract an energy matrix from an energy file. |

gmx-energy(1) | Writes energies to xvg files and display averages. |

gmx-filter(1) | Frequency filter trajectories, useful for making smooth movies. |

gmx-freevolume(1) | Calculate free volume. |

gmx-gangle(1) | Calculate angles. |

gmx-genconf(1) | Multiply a conformation in 'random' orientations. |

gmx-genion(1) | Generate monoatomic ions on energetically favorable positions. |

gmx-genrestr(1) | Generate position restraints or distance restraints for index groups. |

gmx-grompp(1) | Make a run input file. |

gmx-gyrate(1) | Calculate the radius of gyration. |

gmx-h2order(1) | Compute the orientation of water molecules. |

gmx-hbond(1) | Compute and analyze hydrogen bonds. |

gmx-helix(1) | Calculate basic properties of alpha helices. |

gmx-helixorient(1) | Calculate local pitch/bending/rotation/orientation inside helices. |

gmx-help(1) | Print help information. |

gmx-hydorder(1) | Compute tetrahedrality parameters around a given atom. |

gmx-insert-molecules(1) | Insert molecules into existing vacancies. |

gmx-lie(1) | Estimate free energy from linear combinations. |

gmx-make_edi(1) | Generate input files for essential dynamics sampling. |

gmx-make_ndx(1) | Make index files. |

gmx-mdmat(1) | Calculate residue contact maps. |

gmx-mdrun(1) | Perform a simulation, do a normal mode analysis or an energy minimization. |

gmx-mindist(1) | Calculate the minimum distance between two groups. |

gmx-mk_angndx(1) | Generate index files for 'gmx angle'. |

gmx-morph(1) | Interpolate linearly between conformations. |

gmx-msd(1) | Calculates mean square displacements. |

gmx-nmeig(1) | Diagonalize the Hessian for normal mode analysis. |

gmx-nmens(1) | Generate an ensemble of structures from the normal modes. |

gmx-nmr(1) | Analyze nuclear magnetic resonance properties from an energy file. |

gmx-nmtraj(1) | Generate a virtual oscillating trajectory from an eigenvector. |

gmx-order(1) | Compute the order parameter per atom for carbon tails. |

gmx-pairdist(1) | Calculate pairwise distances between groups of positions. |

gmx-pdb2gmx(1) | Convert coordinate files to topology and FF-compliant coordinate files. |

gmx-pme_error(1) | Estimate the error of using PME with a given input file. |

gmx-polystat(1) | Calculate static properties of polymers. |

gmx-potential(1) | Calculate the electrostatic potential across the box. |

gmx-principal(1) | Calculate principal axes of inertia for a group of atoms. |

gmx-rama(1) | Compute Ramachandran plots. |

gmx-rdf(1) | Calculate radial distribution functions. |

gmx-rms(1) | Calculate RMSDs with a reference structure and RMSD matrices. |

gmx-rmsdist(1) | Calculate atom pair distances averaged with power -2, -3 or -6. |

gmx-rmsf(1) | Calculate atomic fluctuations. |

gmx-rotacf(1) | Calculate the rotational correlation function for molecules. |

gmx-rotmat(1) | Plot the rotation matrix for fitting to a reference structure. |

gmx-saltbr(1) | Compute salt bridges. |

gmx-sans(1) | Compute small angle neutron scattering spectra. |

gmx-sasa(1) | Compute solvent accessible surface area. |

gmx-saxs(1) | Compute small angle X-ray scattering spectra. |

gmx-select(1) | Print general information about selections. |

gmx-sham(1) | Compute free energies or other histograms from histograms. |

gmx-sigeps(1) | Convert c6/12 or c6/cn combinations to and from sigma/epsilon. |

gmx-solvate(1) | Solvate a system. |

gmx-sorient(1) | Analyze solvent orientation around solutes. |

gmx-spatial(1) | Calculate the spatial distribution function. |

gmx-spol(1) | Analyze solvent dipole orientation and polarization around solutes. |

gmx-tcaf(1) | Calculate viscosities of liquids. |

gmx-traj(1) | Plot x, v, f, box, temperature and rotational energy from trajectories. |

gmx-trajectory(1) | Print coordinates, velocities, and/or forces for selections. |

gmx-trjcat(1) | Concatenate trajectory files. |

gmx-trjconv(1) | Convert and manipulates trajectory files. |

gmx-trjorder(1) | Order molecules according to their distance to a group. |

gmx-tune_pme(1) | Time mdrun as a function of PME ranks to optimize settings. |

gmx-vanhove(1) | Compute Van Hove displacement and correlation functions. |

gmx-velacc(1) | Calculate velocity autocorrelation functions. |

gmx-view(1) | View a trajectory on an X-Windows terminal. |

gmx-wham(1) | Perform weighted histogram analysis after umbrella sampling. |

gmx-wheel(1) | Plot helical wheels. |

gmx-x2top(1) | Generate a primitive topology from coordinates. |

gmx-xpm2ps(1) | Convert XPM (XPixelMap) matrices to postscript or XPM. |

gmx_d(1) ↣ gmx(1) | Molecular dynamics simulation suite. |