HEAD|Generating topologies and coordinates editconf|edits the box and writes subgroups g_protonate|protonates structures g_x2top|generates a primitive topology

from coordinates genbox|solvates a system genconf|multiplies a conformation in 'random' orientations genion|generates mono atomic ions on energetically favorable positions genrestr|generates position restraints or distance restraints for index groups pdb2gmx|converts coordinate files to topology and FF-compliant coordinate files END HEAD|Running a simulation grompp|makes a run input file mdrun|performs a simulation, do a normal mode analysis or an energy minimization tpbconv|makes a run input file for restarting a crashed run END HEAD|Viewing trajectories g_nmtraj|generate a virtual trajectory from an eigenvector ngmx|displays a trajectory END HEAD|Processing energies g_enemat|extracts an energy matrix from an energy file g_energy|writes energies to xvg files and displays averages mdrun|with -rerun (re)calculates energies for trajectory frames END HEAD|Converting files editconf|converts and manipulates structure files eneconv|converts energy files g_sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon trjcat|concatenates trajectory files trjconv|converts and manipulates trajectory files xpm2ps|converts XPM matrices to encapsulated postscript (or XPM) END HEAD|Tools g_analyze|analyzes data sets g_dyndom|interpolate and extrapolate structure rotations g_filter|frequency filters trajectories, useful for making smooth movies g_lie|free energy estimate from linear combinations g_morph|linear interpolation of conformations g_pme_error|estimates the error of using PME with a given input file g_select|selects groups of atoms based on flexible textual selections g_sham|read/write xmgr and xvgr data sets g_spatial|calculates the spatial distribution function g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory g_tune_pme|time mdrun as a function of PME nodes to optimize settings g_wham|weighted histogram analysis after umbrella sampling gmxcheck|checks and compares files gmxdump|makes binary files human readable make_ndx|makes index files mk_angndx|generates index files for g_angle trjorder|orders molecules according to their distance to a group xpm2ps|convert XPM (XPixelMap) file to postscript END HEAD|Distances between structures g_cluster|clusters structures

g_confrms|fits two structures and calculates the rmsd g_rms|calculates rmsd's with a reference structure and rmsd matrices g_rmsf|calculates atomic fluctuations END HEAD|Distances in structures over time g_bond|calculates distances between atoms g_dist|calculates the distances between the centers of mass of two groups g_mindist|calculates the minimum distance between two groups g_mdmat|calculates residue contact maps g_polystat|calculates static properties of polymers g_rmsdist|calculates atom pair distances averaged with power -2, -3 or -6 END HEAD|Mass distribution properties over time g_gyrate|calculates the radius of gyration g_msd|calculates mean square displacements g_polystat|calculates static properties of polymers g_rdf|calculates radial distribution functions g_rotacf|calculates the rotational correlation function for molecules g_rotmat|plots the rotation matrix for fitting to a reference structure g_traj|plots x, v, f, box, temperature and rotational energy g_vanhove|calculates Van Hove displacement functions END HEAD|Analyzing bonded interactions g_angle|calculates distributions and correlations for angles and dihedrals g_bond|calculates bond length distributions g_dih|analyzes dihedral transitions mk_angndx|generates index files for g_angle END HEAD|Structural properties g_anadock|cluster structures from Autodock runs g_bundle|analyzes bundles of axes, e.g. helices g_clustsize|calculate size distributions of atomic clusters g_disre|analyzes distance restraints g_hbond|computes and analyzes hydrogen bonds g_order|computes the order parameter per atom for carbon tails g_principal|calculates axes of inertia for a group of atoms g_rdf|calculates radial distribution functions g_saltbr|computes salt bridges g_sas|computes solvent accessible surface area g_sgangle|computes the angle and distance between two groups g_sorient|analyzes solvent orientation around solutes g_spol|analyzes solvent dipole orientation and polarization around solutes END HEAD|Kinetic properties g_bar|calculates free energy difference estimates through Bennett's acceptance r atio g_current|calculate current autocorrelation function of system g_principal|calculate principal axes of inertion for a group of atoms g_tcaf|calculates viscosities of liquids g_traj|plots x, v, f, box, temperature and rotational energy g_vanhove|compute Van Hove correlation function g_velacc|calculates velocity autocorrelation functions END HEAD|Electrostatic properties

g_current|calculates dielectric constants for charged systems g_dielectric|calculates frequency dependent dielectric constants g_dipoles|computes the total dipole plus fluctuations g_potential|calculates the electrostatic potential across the box g_spol|analyze dipoles around a solute genion|generates mono atomic ions on energetically favorable positions END HEAD|Protein-specific analysis do_dssp|assigns secondary structure and calculates solvent accessible surface ar ea g_chi|calculates everything you want to know about chi and other dihedrals g_helix|calculates basic properties of alpha helices g_helixorient|calculates local pitch/bending/rotation/orientation inside helices g_rama|computes Ramachandran plots g_wheel|plots helical wheels g_xrama|shows animated Ramachandran plots END HEAD|Interfaces g_bundle|analyzes bundles of axes, e.g. transmembrane helices g_density|calculates the density of the system g_densmap|calculates 2D planar or axial-radial density maps g_densorder|calculate surface fluctuations g_h2order|computes the orientation of water molecules g_hydorder|computes tetrahedrality parameters around a given atom g_order|computes the order parameter per atom for carbon tails g_membed|embeds a protein into a lipid bilayer g_potential|calculates the electrostatic potential across the box END HEAD|Covariance analysis g_anaeig|analyzes the eigenvectors g_covar|calculates and diagonalizes the covariance matrix make_edi|generate input files for essential dynamics sampling END HEAD|Normal modes g_anaeig|analyzes the normal modes g_nmeig|diagonalizes the Hessian g_nmtraj|generate oscillating trajectory of an eigenmode g_nmens|generates an ensemble of structures from the normal modes grompp|makes a run input file mdrun|finds a potential energy minimum and calculates the Hessian END