
VERSION 4.6.1 Tues 5 Mar 2013 
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 FFcompliant coordinate files 
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 
Viewing trajectories  
g_nmtraj  generate a virtual trajectory from an eigenvector 
ngmx  displays a trajectory 
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 
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) 
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 
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 
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 
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_sans  computes the small angle neutron scattering spectra 
g_traj  plots x, v, f, box, temperature and rotational energy 
g_vanhove  calculates Van Hove displacement functions 
Analyzing bonded interactions  
g_angle  calculates distributions and correlations for angles and dihedrals 
g_bond  calculates bond length distributions 
mk_angndx  generates index files for g_angle 
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 
Kinetic properties  
g_bar  calculates free energy difference estimates through Bennett's acceptance ratio 
g_current  calculate current autocorrelation function of system 
g_dos  analyzes density of states and properties based on that 
g_dyecoupl  extracts dye dynamics from trajectories 
g_kinetics  analyzes kinetic constants from properties based on the Eyring model 
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 
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 
Proteinspecific 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 
g_wheel  plots helical wheels 
g_xrama  shows animated Ramachandran plots 
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 axialradial 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 
Covariance analysis  
g_anaeig  analyzes the eigenvectors 
g_covar  calculates and diagonalizes the covariance matrix 
make_edi  generate input files for essential dynamics sampling 
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 