1 HEAD|Generating topologies and coordinates
2 pdb2gmx|converts pdb files to topology and coordinate files
3 g_x2top|generates a primitive topology from coordinates
4 editconf|edits the box and writes subgroups
5 genbox|solvates a system
6 genion|generates mono atomic ions on energetically favorable positions
7 genconf|multiplies a conformation in 'random' orientations
8 genrestr|generates position restraints or distance restraints for index groups
9 g_protonate|protonates structures
12 HEAD|Running a simulation
13 grompp|makes a run input file
14 tpbconv|makes a run input file for restarting a crashed run
15 mdrun|performs a simulation, do a normal mode analysis or an energy minimization
18 HEAD|Viewing trajectories
19 ngmx|displays a trajectory
20 g_highway|X Window System gadget for highway simulations
21 g_nmtraj|generate a virtual trajectory from an eigenvector
24 HEAD|Processing energies
25 g_energy|writes energies to xvg files and displays averages
26 g_enemat|extracts an energy matrix from an energy file
27 mdrun|with -rerun (re)calculates energies for trajectory frames
31 editconf|converts and manipulates structure files
32 trjconv|converts and manipulates trajectory files
33 trjcat|concatenates trajectory files
34 eneconv|converts energy files
35 xpm2ps|converts XPM matrices to encapsulated postscript (or XPM)
36 g_sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
40 make_ndx|makes index files
41 mk_angndx|generates index files for g_angle
42 gmxcheck|checks and compares files
43 gmxdump|makes binary files human readable
44 g_traj|plots x, v and f of selected atoms/groups (and more) from a trajectory
45 g_analyze|analyzes data sets
46 trjorder|orders molecules according to their distance to a group
47 g_filter|frequency filters trajectories, useful for making smooth movies
48 g_lie|free energy estimate from linear combinations
49 g_dyndom|interpolate and extrapolate structure rotations
50 g_morph|linear interpolation of conformations
51 g_wham|weighted histogram analysis after umbrella sampling
52 xpm2ps|convert XPM (XPixelMap) file to postscript
53 g_sham|read/write xmgr and xvgr data sets
54 g_spatial|calculates the spatial distribution function
55 g_select|selects groups of atoms based on flexible textual selections
56 g_pme_error|estimates the error of using PME with a given input file
57 g_tune_pme|time mdrun as a function of PME nodes to optimize settings
60 HEAD|Distances between structures
61 g_rms|calculates rmsd's with a reference structure and rmsd matrices
62 g_confrms|fits two structures and calculates the rmsd
63 g_cluster|clusters structures
64 g_rmsf|calculates atomic fluctuations
67 HEAD|Distances in structures over time
68 g_mindist|calculates the minimum distance between two groups
69 g_dist|calculates the distances between the centers of mass of two groups
70 g_bond|calculates distances between atoms
71 g_mdmat|calculates residue contact maps
72 g_polystat|calculates static properties of polymers
73 g_rmsdist|calculates atom pair distances averaged with power -2, -3 or -6
76 HEAD|Mass distribution properties over time
77 g_traj|plots x, v, f, box, temperature and rotational energy
78 g_gyrate|calculates the radius of gyration
79 g_msd|calculates mean square displacements
80 g_polystat|calculates static properties of polymers
81 g_rotacf|calculates the rotational correlation function for molecules
82 g_rdf|calculates radial distribution functions
83 g_rotmat|plots the rotation matrix for fitting to a reference structure
84 g_vanhove|calculates Van Hove displacement functions
87 HEAD|Analyzing bonded interactions
88 g_bond|calculates bond length distributions
89 mk_angndx|generates index files for g_angle
90 g_angle|calculates distributions and correlations for angles and dihedrals
91 g_dih|analyzes dihedral transitions
94 HEAD|Structural properties
95 g_hbond|computes and analyzes hydrogen bonds
96 g_saltbr|computes salt bridges
97 g_sas|computes solvent accessible surface area
98 g_order|computes the order parameter per atom for carbon tails
99 g_principal|calculates axes of inertia for a group of atoms
100 g_rdf|calculates radial distribution functions
101 g_sgangle|computes the angle and distance between two groups
102 g_sorient|analyzes solvent orientation around solutes
103 g_spol|analyzes solvent dipole orientation and polarization around solutes
104 g_bundle|analyzes bundles of axes, e.g. helices
105 g_disre|analyzes distance restraints
106 g_clustsize|calculate size distributions of atomic clusters
107 g_anadock|cluster structures from Autodock runs
110 HEAD|Kinetic properties
111 g_traj|plots x, v, f, box, temperature and rotational energy
112 g_velacc|calculates velocity autocorrelation functions
113 g_tcaf|calculates viscosities of liquids
114 g_bar|calculates free energy difference estimates through Bennett's acceptance ratio
115 g_current|calculate current autocorrelation function of system
116 g_vanhove|compute Van Hove correlation function
117 g_principal|calculate principal axes of inertion for a group of atoms
120 HEAD|Electrostatic properties
121 genion|generates mono atomic ions on energetically favorable positions
122 g_potential|calculates the electrostatic potential across the box
123 g_dipoles|computes the total dipole plus fluctuations
124 g_dielectric|calculates frequency dependent dielectric constants
125 g_current|calculates dielectric constants for charged systems
126 g_spol|analyze dipoles around a solute
129 HEAD|Protein specific analysis
130 do_dssp|assigns secondary structure and calculates solvent accessible surface area
131 g_chi|calculates everything you want to know about chi and other dihedrals
132 g_helix|calculates basic properties of alpha helices
133 g_helixorient|calculates local pitch/bending/rotation/orientation inside helices
134 g_rama|computes Ramachandran plots
135 g_xrama|shows animated Ramachandran plots
136 g_wheel|plots helical wheels
140 g_potential|calculates the electrostatic potential across the box
141 g_density|calculates the density of the system
142 g_densmap|calculates 2D planar or axial-radial density maps
143 g_order|computes the order parameter per atom for carbon tails
144 g_h2order|computes the orientation of water molecules
145 g_bundle|analyzes bundles of axes, e.g. transmembrane helices
146 g_membed|embeds a protein into a lipid bilayer
150 HEAD|Covariance analysis
151 g_covar|calculates and diagonalizes the covariance matrix
152 g_anaeig|analyzes the eigenvectors
153 make_edi|generate input files for essential dynamics sampling
157 grompp|makes a run input file
158 mdrun|finds a potential energy minimum
159 mdrun|calculates the Hessian
160 g_nmeig|diagonalizes the Hessian
161 g_nmtraj|generate oscillating trajectory of an eigenmode
162 g_anaeig|analyzes the normal modes
163 g_nmens|generates an ensemble of structures from the normal modes