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GROMACS 4.6.1
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Tues 5 Mar 2013
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VERSION 4.6.1 Tues 5 Mar 2013 |
| Generating topologies and coordinates | |
| editconf | edits the box and writes subgroups |
| g_protonate | protonates structures |
| g_x2top | generates a primitive topology from coordinates |
| genbox | solvates a system |
| genconf | multiplies a conformation in 'random' orientations |
| genion | generates mono atomic ions on energetically favorable positions |
| genrestr | generates position restraints or distance restraints for index groups |
| pdb2gmx | converts coordinate files to topology and FF-compliant coordinate files |
| Running a simulation | |
| grompp | makes a run input file |
| mdrun | performs a simulation, do a normal mode analysis or an energy minimization |
| tpbconv | makes a run input file for restarting a crashed run |
| Viewing trajectories | |
| g_nmtraj | generate a virtual trajectory from an eigenvector |
| ngmx | displays a trajectory |
| Processing energies | |
| g_enemat | extracts an energy matrix from an energy file |
| g_energy | writes energies to xvg files and displays averages |
| mdrun | with -rerun (re)calculates energies for trajectory frames |
| Converting files | |
| editconf | converts and manipulates structure files |
| eneconv | converts energy files |
| g_sigeps | convert c6/12 or c6/cn combinations to and from sigma/epsilon |
| trjcat | concatenates trajectory files |
| trjconv | converts and manipulates trajectory files |
| xpm2ps | converts XPM matrices to encapsulated postscript (or XPM) |
| Tools | |
| g_analyze | analyzes data sets |
| g_dyndom | interpolate and extrapolate structure rotations |
| g_filter | frequency filters trajectories, useful for making smooth movies |
| g_lie | free energy estimate from linear combinations |
| g_morph | linear interpolation of conformations |
| g_pme_error | estimates the error of using PME with a given input file |
| g_select | selects groups of atoms based on flexible textual selections |
| g_sham | read/write xmgr and xvgr data sets |
| g_spatial | calculates the spatial distribution function |
| g_traj | plots x, v and f of selected atoms/groups (and more) from a trajectory |
| g_tune_pme | time mdrun as a function of PME nodes to optimize settings |
| g_wham | weighted histogram analysis after umbrella sampling |
| gmxcheck | checks and compares files |
| gmxdump | makes binary files human readable |
| make_ndx | makes index files |
| mk_angndx | generates index files for g_angle |
| trjorder | orders molecules according to their distance to a group |
| xpm2ps | convert XPM (XPixelMap) file to postscript |
| Distances between structures | |
| g_cluster | clusters structures |
| g_confrms | fits two structures and calculates the rmsd |
| g_rms | calculates rmsd's with a reference structure and rmsd matrices |
| g_rmsf | calculates atomic fluctuations |
| Distances in structures over time | |
| g_bond | calculates distances between atoms |
| g_dist | calculates the distances between the centers of mass of two groups |
| g_mindist | calculates the minimum distance between two groups |
| 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_gyrate | calculates the radius of gyration |
| g_msd | calculates mean square displacements |
| g_polystat | calculates static properties of polymers |
| g_rdf | calculates radial distribution functions |
| g_rotacf | calculates the rotational correlation function for molecules |
| g_rotmat | plots the rotation matrix for fitting to a reference structure |
| g_sans | computes the small angle neutron scattering spectra |
| g_traj | plots x, v, f, box, temperature and rotational energy |
| g_vanhove | calculates Van Hove displacement functions |
| Analyzing bonded interactions | |
| g_angle | calculates distributions and correlations for angles and dihedrals |
| g_bond | calculates bond length distributions |
| mk_angndx | generates index files for g_angle |
| Structural properties | |
| g_anadock | cluster structures from Autodock runs |
| g_bundle | analyzes bundles of axes, e.g. helices |
| g_clustsize | calculate size distributions of atomic clusters |
| g_disre | analyzes distance restraints |
| g_hbond | computes and analyzes hydrogen bonds |
| 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_saltbr | computes salt bridges |
| g_sas | computes solvent accessible surface area |
| 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 |
| Kinetic properties | |
| g_bar | calculates free energy difference estimates through Bennett's acceptance ratio |
| g_current | calculate current autocorrelation function of system |
| g_dos | analyzes density of states and properties based on that |
| g_dyecoupl | extracts dye dynamics from trajectories |
| g_kinetics | analyzes kinetic constants from properties based on the Eyring model |
| g_principal | calculate principal axes of inertion for a group of atoms |
| g_tcaf | calculates viscosities of liquids |
| g_traj | plots x, v, f, box, temperature and rotational energy |
| g_vanhove | compute Van Hove correlation function |
| g_velacc | calculates velocity autocorrelation functions |
| Electrostatic properties | |
| g_current | calculates dielectric constants for charged systems |
| g_dielectric | calculates frequency dependent dielectric constants |
| g_dipoles | computes the total dipole plus fluctuations |
| g_potential | calculates the electrostatic potential across the box |
| g_spol | analyze dipoles around a solute |
| genion | generates mono atomic ions on energetically favorable positions |
| 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_wheel | plots helical wheels |
| g_xrama | shows animated Ramachandran plots |
| Interfaces | |
| g_bundle | analyzes bundles of axes, e.g. transmembrane helices |
| g_density | calculates the density of the system |
| g_densmap | calculates 2D planar or axial-radial density maps |
| g_densorder | calculate surface fluctuations |
| g_h2order | computes the orientation of water molecules |
| g_hydorder | computes tetrahedrality parameters around a given atom |
| g_order | computes the order parameter per atom for carbon tails |
| g_membed | embeds a protein into a lipid bilayer |
| g_potential | calculates the electrostatic potential across the box |
| Covariance analysis | |
| g_anaeig | analyzes the eigenvectors |
| g_covar | calculates and diagonalizes the covariance matrix |
| make_edi | generate input files for essential dynamics sampling |
| Normal modes | |
| g_anaeig | analyzes the normal modes |
| g_nmeig | diagonalizes the Hessian |
| g_nmtraj | generate oscillating trajectory of an eigenmode |
| g_nmens | generates an ensemble of structures from the normal modes |
| grompp | makes a run input file |
| mdrun | finds a potential energy minimum and calculates the Hessian |