| 
 | VERSION 3.3.1 Thu 11 May 2006 | 
| Generating topologies and coordinates | |
| pdb2gmx | converts pdb files to topology and coordinate files | 
| x2top | generates a primitive topology from coordinates | 
| editconf | edits the box and writes subgroups | 
| genbox | solvates a system | 
| genion | generates mono atomic ions on energetically favorable positions | 
| genconf | multiplies a conformation in 'random' orientations | 
| genpr | generates position restraints for index groups | 
| protonate | protonates structures | 
| Running a simulation | |
| grompp | makes a run input file | 
| tpbconv | makes a run input file for restarting a crashed run | 
| mdrun | performs a simulation | 
| Viewing trajectories | |
| ngmx | displays a trajectory | 
| trjconv | converts trajectories to e.g. pdb which can be viewed with e.g. rasmol | 
| Processing energies | |
| g_energy | writes energies to xvg files and displays averages | 
| g_enemat | extracts an energy matrix from an energy file | 
| mdrun | with -rerun (re)calculates energies for trajectory frames | 
| Converting files | |
| editconf | converts and manipulates structure files | 
| trjconv | converts and manipulates trajectory files | 
| trjcat | concatenates trajectory files | 
| eneconv | converts energy files | 
| xmp2ps | converts XPM matrices to encapsulated postscript (or XPM) | 
| Tools | |
| make_ndx | makes index files | 
| mk_angndx | generates index files for g_angle | 
| gmxcheck | checks and compares files | 
| gmxdump | makes binary files human readable | 
| g_traj | plots x, v and f of selected atoms/groups (and more) from a trajectory | 
| g_analyze | analyzes data sets | 
| trjorder | orders molecules according to their distance to a group | 
| g_filter | frequency filters trajectories, useful for making smooth movies | 
| g_lie | free energy estimate from linear combinations | 
| g_dyndom | interpolate and extrapolate structure rotations | 
| g_morph | linear interpolation of conformations | 
| g_wham | weighted histogram analysis after umbrella sampling | 
| ffscan | scan and modify force field data for a single point energy calculation | 
| xpm2ps | convert XPM (XPixelMap) file to postscript | 
| Distances between structures | |
| g_rms | calculates rmsd's with a reference structure and rmsd matrices | 
| g_confrms | fits two structures and calculates the rmsd | 
| g_cluster | clusters structures | 
| g_rmsf | calculates atomic fluctuations | 
| disco | distance geometry calculation with the CONCOORD algorithm | 
| cdist | create input for disco | 
| Distances in structures over time | |
| g_mindist | calculates the minimum distance between two groups | 
| g_dist | calculates the distances between the centers of mass of two groups | 
| g_bond | calculates distances between atoms | 
| g_mdmat | calculates residue contact maps | 
| g_rmsdist | calculates atom pair distances averaged with power 2, -3 or -6 | 
| Mass distribution properties over time | |
| g_traj | plots x, v, f, box, temperature and rotational energy | 
| g_gyrate | calculates the radius of gyration | 
| g_msd | calculates mean square displacements | 
| g_rotacf | calculates the rotational correlation function for molecules | 
| g_rdf | calculates radial distribution functions | 
| Analyzing bonded interactions | |
| g_bond | calculates bond length distributions | 
| mk_angndx | generates index files for g_angle | 
| g_angle | calculates distributions and correlations for angles and dihedrals | 
| g_dih | analyzes dihedral transitions | 
| Structural properties | |
| g_hbond | computes and analyzes hydrogen bonds | 
| g_saltbr | computes salt bridges | 
| g_sas | computes solvent accessible surface area | 
| g_order | computes the order parameter per atom for carbon tails | 
| g_sgangle | computes the angle and distance between two groups | 
| g_sorient | analyzes solvent orientation around solutes | 
| g_bundle | analyzes bundles of axes, e.g. helices | 
| g_disre | analyzes distance restraints | 
| g_clustsize | calculate size distributions of atomic clusters | 
| disco | distance geometry calculation with the CONCOORD algorithm | 
| cdist | create input for disco | 
| anadock | cluster structures from Autodock runs | 
| Kinetic properties | |
| g_traj | plots x, v, f, box, temperature and rotational energy | 
| g_velacc | calculates velocity autocorrelation functions | 
| g_tcaf | calculates viscosities of liquids | 
| Electrostatic properties | |
| genion | generates mono atomic ions on energetically favorable positions | 
| g_potential | calculates the electrostatic potential across the box | 
| g_dipoles | computes the total dipole plus fluctuations | 
| g_dielectric | calculates frequency dependent dielectric constants | 
| Protein specific analysis | |
| do_dssp | assigns secondary structure and calculates solvent accessible surface area | 
| g_chi | calculates everything you want to know about chi and other dihedrals | 
| g_helix | calculates everything you want to know about helices | 
| g_rama | computes Ramachandran plots | 
| xrama | shows animated Ramachandran plots | 
| wheel | plots helical wheels | 
| Interfaces | |
| g_potential | calculates the electrostatic potential across the box | 
| g_density | calculates the density of the system | 
| g_densmap | calculates 2D planar or axial-radial density maps | 
| g_order | computes the order parameter per atom for carbon tails | 
| g_h2order | computes the orientation of water molecules | 
| g_bundle | analyzes bundles of axes, e.g. transmembrane helices | 
| Covariance analysis | |
| g_covar | calculates and diagonalizes the covariance matrix | 
| g_anaeig | analyzes the eigenvectors | 
| make_edi | generate input files for essential dynamics sampling | 
| Normal modes | |
| grompp | makes a run input file | 
| mdrun | finds a potential energy minimum | 
| mdrun | calculates the Hessian | 
| g_nmeig | diagonalizes the Hessian | 
| g_nmtraj | generate oscillating trajectory of an eigenmode | 
| g_anaeig | analyzes the normal modes | 
| g_nmens | generates an ensemble of structures from the normal modes |