GROMACS 4.5 Online Reference

| ## 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

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