GROMACS 4.0.7 Online Reference

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>>>>>>> bfc69dd... Configure now uses the --htmldir option. Online Reference

VERSION 4.0.7
Sun 18 Jan 2009


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
genrestr	generates position restraints or distance 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_polystat	calculates static properties of polymers
g_rmsdist	calculates atom pair distances averaged with power 2, -3 or -6

g_traj plots x, v, f, box, temperature and rotational energy

For proteins in water (or other solvent) the route is described above. For other systemd (eg. pure liquids or mixtures) one needs:

The atomic coordinates, which can be generated by a variety of interactive programs (eg. Quanta, Cerius, HyperChem). Coordinate files can be exported in pdb-format and converted to .gro format by the editconf program:

editconf -f conf.pdb -o conf.gro

where conf.gro is the coordinatefile, or converted back to pdb-format by

editconf -f conf.gro -o conf.pdb

where conf is a file with coordinates, and conf.pdb is the target file in .pdb format. NOTE: Make sure that the graphics programs export whole molecules instead of molecules that are cut in pieces (due to the periodic boundary conditions) If you have the coordinates of single molecules, you can also build systems (pure liquids or mixtures) with genbox. In contrast, the program genconf produces the lattice of molecules with random displacements.
The topology you have to build yourself. Of course you can include topologies of part of your system (eg. spc.itp, decane.itp etc.)