Provided by: gromacs-data_4.6.5-1build1_all bug


       gromacs - molecular dynamics simulation suite


       GROMACS (the Groningen Machine for Chemical Simulations) is a full-featured suite of
       programs to perform molecular dynamics simulations - in other words, to simulate the
       behavior of systems with hundreds to millions of particles, using Newtonian equations of
       motion.  It is primarily used for research on proteins, lipids, and polymers, but can be
       applied to a wide variety of chemical and biological research questions.


       The following commands make up the GROMACS suite.  Please refer to their individual man
       pages for further details.

       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)


         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


         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


       Consult the manual at <> for an introduction to
       molecular dynamics in general and GROMACS in particular, as well as an overview of the
       individual programs.

       The shorter HTML reference and GROMACS FAQ are available in /usr/share/doc/gromacs/html/ .

       Tutorial files and other miscellaneous references are stored in /usr/share/gromacs/ .


       The development of GROMACS is mainly funded by academic research grants.  To help us fund
       development, the authors humbly ask that you cite the GROMACS papers:

       H.J.C. Berendsen, D. van der Spoel and R. van Drunen.  GROMACS: A message-passing parallel
       molecular dynamics implementation.  Comp. Phys. Comm. 91, 43-56 (1995)

       Erik Lindahl, Berk Hess and David van der Spoel.  GROMACS 3.0: A package for molecular
       simulation and trajectory analysis.  J. Mol. Mod. 7, 306-317 (2001)

       B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl.  GROMACS 4: Algorithms for Highly
       Efficient, Load-Balanced, and Scalable Molecular Simulation.  J. Chem. Theory Comput. 4,
       3, 435-447 (2008), <>


       Current developers:

       David van der Spoel <>
       Berk Hess <>
       Erik Lindahl <>

       A full list of present and former contributors is available at <>

       This manual page is largely based on the GROMACS online reference, and was prepared in
       this format by Nicholas Breen <>.


       GROMACS has no major known bugs, but be warned that it stresses your CPU more than most
       software.  Systems with slightly flaky hardware may prove unreliable while running heavy-
       duty simulations.  If at all possible, please try to reproduce bugs on another machine
       before reporting them.