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GROMACS 3.3
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Sun 28 Aug 2005
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VERSION 3.3 Sun 28 Aug 2005 |
| 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_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 |
| 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 |