GROMACS 4.6.1
Online Reference

VERSION 4.6.1
Tues 5 Mar 2013

General

Getting Started

Flow Chart

File Formats

mdp options

FAQ

Programs

Options

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_densorder
g_dielectric
g_dipoles
g_disre
g_dist
g_dos
g_dyecoupl
g_dyndom
g_enemat
g_energy
g_filter
g_gyrate
g_h2order
g_hbond
g_helix
g_helixorient
g_hydorder
g_kinetics
g_lie
g_luck
g_mdmat
g_membed
g_mindist
g_morph
g_msd
g_nmeig
g_nmens
g_nmtraj
g_options
g_order
g_pme_error
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_sans
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
genbox
genconf
genion
genrestr
gmxcheck
gmxdump
grompp
make_edi
make_ndx
mdrun
mk_angndx
pdb2gmx
tpbconv
trjcat
trjconv
trjorder
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
editconfedits the box and writes subgroups
g_protonateprotonates structures
g_x2topgenerates a primitive topology from coordinates
genboxsolvates a system
genconfmultiplies a conformation in 'random' orientations
geniongenerates mono atomic ions on energetically favorable positions
genrestrgenerates position restraints or distance restraints for index groups
pdb2gmxconverts coordinate files to topology and FF-compliant coordinate files
                      
Running a simulation
gromppmakes a run input file
mdrunperforms a simulation, do a normal mode analysis or an energy minimization
tpbconvmakes a run input file for restarting a crashed run
                      
Viewing trajectories
g_nmtrajgenerate a virtual trajectory from an eigenvector
ngmxdisplays a trajectory
                      
Processing energies
g_enematextracts an energy matrix from an energy file
g_energywrites energies to xvg files and displays averages
mdrunwith -rerun (re)calculates energies for trajectory frames
                      
Converting files
editconfconverts and manipulates structure files
eneconvconverts energy files
g_sigepsconvert c6/12 or c6/cn combinations to and from sigma/epsilon
trjcatconcatenates trajectory files
trjconvconverts and manipulates trajectory files
xpm2psconverts XPM matrices to encapsulated postscript (or XPM)
                      
Tools
g_analyzeanalyzes data sets
g_dyndominterpolate and extrapolate structure rotations
g_filterfrequency filters trajectories, useful for making smooth movies
g_liefree energy estimate from linear combinations
g_morphlinear interpolation of conformations
g_pme_errorestimates the error of using PME with a given input file
g_selectselects groups of atoms based on flexible textual selections
g_shamread/write xmgr and xvgr data sets
g_spatialcalculates the spatial distribution function
g_trajplots x, v and f of selected atoms/groups (and more) from a trajectory
g_tune_pmetime mdrun as a function of PME nodes to optimize settings
g_whamweighted histogram analysis after umbrella sampling
gmxcheckchecks and compares files
gmxdumpmakes binary files human readable
make_ndxmakes index files
mk_angndxgenerates index files for g_angle
trjorderorders molecules according to their distance to a group
xpm2psconvert XPM (XPixelMap) file to postscript
                      
Distances between structures
g_clusterclusters structures
g_confrmsfits two structures and calculates the rmsd
g_rmscalculates rmsd's with a reference structure and rmsd matrices
g_rmsfcalculates atomic fluctuations
                      
Distances in structures over time
g_bondcalculates distances between atoms
g_distcalculates the distances between the centers of mass of two groups
g_mindistcalculates the minimum distance between two groups
g_mdmatcalculates residue contact maps
g_polystatcalculates static properties of polymers
g_rmsdistcalculates atom pair distances averaged with power -2, -3 or -6
                      
Mass distribution properties over time
g_gyratecalculates the radius of gyration
g_msdcalculates mean square displacements
g_polystatcalculates static properties of polymers
g_rdfcalculates radial distribution functions
g_rotacfcalculates the rotational correlation function for molecules
g_rotmatplots the rotation matrix for fitting to a reference structure
g_sanscomputes the small angle neutron scattering spectra
g_trajplots x, v, f, box, temperature and rotational energy
g_vanhovecalculates Van Hove displacement functions
                      
Analyzing bonded interactions
g_anglecalculates distributions and correlations for angles and dihedrals
g_bondcalculates bond length distributions
mk_angndxgenerates index files for g_angle
                      
Structural properties
g_anadockcluster structures from Autodock runs
g_bundleanalyzes bundles of axes, e.g. helices
g_clustsizecalculate size distributions of atomic clusters
g_disreanalyzes distance restraints
g_hbondcomputes and analyzes hydrogen bonds
g_ordercomputes the order parameter per atom for carbon tails
g_principalcalculates axes of inertia for a group of atoms
g_rdfcalculates radial distribution functions
g_saltbrcomputes salt bridges
g_sascomputes solvent accessible surface area
g_sganglecomputes the angle and distance between two groups
g_sorientanalyzes solvent orientation around solutes
g_spolanalyzes solvent dipole orientation and polarization around solutes
                      
Kinetic properties
g_barcalculates free energy difference estimates through Bennett's acceptance ratio
g_currentcalculate current autocorrelation function of system
g_dosanalyzes density of states and properties based on that
g_dyecouplextracts dye dynamics from trajectories
g_kineticsanalyzes kinetic constants from properties based on the Eyring model
g_principalcalculate principal axes of inertion for a group of atoms
g_tcafcalculates viscosities of liquids
g_trajplots x, v, f, box, temperature and rotational energy
g_vanhovecompute Van Hove correlation function
g_velacccalculates velocity autocorrelation functions
                      
Electrostatic properties
g_currentcalculates dielectric constants for charged systems
g_dielectriccalculates frequency dependent dielectric constants
g_dipolescomputes the total dipole plus fluctuations
g_potentialcalculates the electrostatic potential across the box
g_spolanalyze dipoles around a solute
geniongenerates mono atomic ions on energetically favorable positions
                      
Protein-specific analysis
do_dsspassigns secondary structure and calculates solvent accessible surface area
g_chicalculates everything you want to know about chi and other dihedrals
g_helixcalculates basic properties of alpha helices
g_helixorientcalculates local pitch/bending/rotation/orientation inside helices
g_ramacomputes Ramachandran plots
g_wheelplots helical wheels
g_xramashows animated Ramachandran plots
                      
Interfaces
g_bundleanalyzes bundles of axes, e.g. transmembrane helices
g_densitycalculates the density of the system
g_densmapcalculates 2D planar or axial-radial density maps
g_densordercalculate surface fluctuations
g_h2ordercomputes the orientation of water molecules
g_hydordercomputes tetrahedrality parameters around a given atom
g_ordercomputes the order parameter per atom for carbon tails
g_membedembeds a protein into a lipid bilayer
g_potentialcalculates the electrostatic potential across the box
                      
Covariance analysis
g_anaeiganalyzes the eigenvectors
g_covarcalculates and diagonalizes the covariance matrix
make_edigenerate input files for essential dynamics sampling
                      
Normal modes
g_anaeiganalyzes the normal modes
g_nmeigdiagonalizes the Hessian
g_nmtrajgenerate oscillating trajectory of an eigenmode
g_nmensgenerates an ensemble of structures from the normal modes
gromppmakes a run input file
mdrunfinds a potential energy minimum and calculates the Hessian


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