1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
|
HEAD|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
genrestr|generates position restraints or distance restraints for index groups
protonate|protonates structures
END
HEAD|Running a simulation
grompp|makes a run input file
tpbconv|makes a run input file for restarting a crashed run
mdrun|performs a simulation, do a normal mode analysis or an energy minimization
END
HEAD|Viewing trajectories
ngmx|displays a trajectory
highway|X-windows gadget for highway simulations
END
HEAD|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
END
HEAD|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)
sigeps|convert c6/12 or c6/cn combinations to and from sigma/epsilon
END
HEAD|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
gen_table|generate tables for use by mdrun
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
g_sham|read/write xmgr and xvgr data sets
g_spatial|calculates the spatial distribution function (more control than g_sdf)
g_sdf|calculates the spatial distribution function (faster than g_spatial)
END
HEAD|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
END
HEAD|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_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_traj|plots x, v, f, box, temperature and rotational energy
g_gyrate|calculates the radius of gyration
g_msd|calculates mean square displacements
g_polystat|calculates static properties of polymers
g_rotacf|calculates the rotational correlation function for molecules
g_vanhove|calculates Van Hove displacement functions
END
HEAD|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
END
HEAD|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_principal|calculates axes of inertia for a group of atoms
g_rdf|calculates radial distribution functions
g_sdf|calculates solvent distribution functions
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
g_bundle|analyzes bundles of axes, e.g. helices
g_disre|analyzes distance restraints
g_clustsize|calculate size distributions of atomic clusters
anadock|cluster structures from Autodock runs
END
HEAD|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
g_kinetics|derives information about kinetic processes from you trajectories
END
HEAD|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
g_current|calculates dielectric constants for charged systems
END
HEAD|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 basic properties of alpha helices
g_helixorient|calculates local pitch/bending/rotation/orientation inside helices
g_rama|computes Ramachandran plots
xrama|shows animated Ramachandran plots
wheel|plots helical wheels
END
HEAD|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
END
HEAD|Covariance analysis
g_covar|calculates and diagonalizes the covariance matrix
g_anaeig|analyzes the eigenvectors
make_edi|generate input files for essential dynamics sampling
END
HEAD|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
END
|
