## GROMACS 4.5
Online Reference

VERSION 4.5
Thu 26 Aug 2010

### General

Getting Started
Flow Chart
File Formats
mdp options
FAQ

### Programs

Options
demux.pl
do_dssp
editconf
eneconv
g_anadock
g_anaeig
g_analyze
g_angle
g_bar
g_bond
g_bundle
g_chi
g_cluster
g_clustsize
g_confrms
g_covar
g_current
g_density
g_densmap
g_dielectric
g_dih
g_dipoles
g_disre
g_dist
g_dyndom
g_enemat
g_energy
g_filter
g_gyrate
g_h2order
g_hbond
g_helix
g_helixorient
g_lie
g_luck
g_mdmat
g_membed
g_mindist
g_morph
g_msd
g_nmeig
g_nmens
g_nmtraj
g_order
g_polystat
g_potential
g_principal
g_protonate
g_rama
g_rdf
g_rms
g_rmsdist
g_rmsf
g_rotacf
g_rotmat
g_saltbr
g_sas
g_select
g_sgangle
g_sham
g_sigeps
g_sorient
g_spatial
g_spol
g_tcaf
g_traj
g_tune_pme
g_vanhove
g_velacc
g_wham
g_wheel
g_x2top
g_xrama
genbox
genconf
genion
genrestr
gmxcheck
gmxdump
grompp
make_edi
make_ndx
mdrun
mk_angndx
ngmx
pdb2gmx
tpbconv
trjcat
trjconv
trjorder
xplor2gmx.pl
xpm2ps

### Programs by Topic

Generating topologies and coordinates
Running a simulation
Viewing trajectories
Processing energies
Converting files
Tools
Distances between structures
Distances in structures over time
Mass distribution properties over time
Analyzing bonded interactions
Structural properties
Kinetic properties
Electrostatic properties
Protein specific analysis
Interfaces
Covariance analysis
Normal modes

Generating topologies and coordinates
pdb2gmx | converts pdb files to topology and coordinate files
g_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
g_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, do a normal mode analysis or an energy minimization

Viewing trajectories
ngmx | displays a trajectory
g_highway | X Window System gadget for highway simulations
g_nmtraj | generate a virtual trajectory from an eigenvector

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
xpm2ps | converts XPM matrices to encapsulated postscript (or XPM)
g_sigeps | convert c6/12 or c6/cn combinations to and from sigma/epsilon

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
xpm2ps | convert XPM (XPixelMap) file to postscript
g_sham | read/write xmgr and xvgr data sets
g_spatial | calculates the spatial distribution function
g_select | selects groups of atoms based on flexible textual selections
g_tune_pme | time mdrun as a function of PME nodes to optimize settings

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

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

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_rdf | calculates radial distribution functions
g_rotmat | plots the rotation matrix for fitting to a reference structure
g_vanhove | calculates Van Hove displacement 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_principal | calculates axes of inertia for a group of atoms
g_rdf | calculates radial 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
g_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
g_bar | calculates free energy difference estimates through Bennett's acceptance ratio
g_current | calculate current autocorrelation function of system
g_vanhove | compute Van Hove correlation function
g_principal | calculate principal axes of inertion for a group of atoms

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
g_spol | analyze dipoles around a solute

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
g_xrama | shows animated Ramachandran plots
g_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
g_membed | embeds a protein into a lipid bilayer

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

http://www.gromacs.org