## GROMACS 3.2
Online Reference

VERSION 3.2
Sun 25 Jan 2004

### General

Getting Started
Flow Chart
File Formats
mdp options
FAQ

### Programs

Options
anadock
cdist
disco
do_dssp
editconf
eneconv
ffscan
g_anaeig
g_analyze
g_angle
g_bond
g_bundle
g_chi
g_cluster
g_clustsize
g_confrms
g_covar
g_density
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_lie
g_mdmat
g_mindist
g_morph
g_msd
g_nmeig
g_nmens
g_order
g_potential
g_rama
g_rdf
g_rms
g_rmsdist
g_rmsf
g_rotacf
g_saltbr
g_sas
g_sgangle
g_sorient
g_tcaf
g_traj
g_velacc
g_wham
genbox
genconf
genion
genpr
gmxcheck
gmxdump
grompp
highway
make_ndx
mdrun
mk_angndx
ngmx
pdb2gmx
protonate
tpbconv
trjcat
trjconv
trjorder
wheel
x2top
xpm2ps
xrama

### 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
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
genpr | generates position restraints for index groups
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

Viewing trajectories
ngmx | displays a trajectory
trjconv | converts trajectories to e.g. pdb which can be viewed with e.g. rasmol

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
xmp2ps | converts XPM matrices to encapsulated postscript (or XPM)

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
ffscan | scan and modify force field data for a single point energy calculation
xpm2ps | convert XPM (XPixelMap) file to postscript

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
disco | distance geometry calculation with the CONCOORD algorithm
cdist | create input for disco

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_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_rotacf | calculates the rotational correlation function for molecules
g_rdf | calculates radial distribution 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_sgangle | computes the angle and distance between two groups
g_sorient | analyzes solvent orientation around solutes
g_bundle | analyzes bundles of axes, e.g. helices
g_disre | analyzes distance restraints
g_clustsize | calculate size distributions of atomic clusters
disco | distance geometry calculation with the CONCOORD algorithm
cdist | create input for disco
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

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

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 everything you want to know about helices
g_rama | computes Ramachandran plots
xrama | shows animated Ramachandran plots
wheel | plots helical wheels

Interfaces
g_potential | calculates the electrostatic potential across the box
g_density | calculates the density of the system
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

Covariance analysis
g_covar | calculates and diagonalizes the covariance matrix
g_anaeig | analyzes the eigenvectors

Normal modes
grompp | makes a run input file
mdrun | finds a potential energy minimum
mdrun | calculates the Hessian
g_nmeig | diagonalizes the Hessian
g_anaeig | analyzes the normal modes
g_nmens | generates an ensemble of structures from the normal modes

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