Provided by: gromacs-data_4.0.7-1_all bug

NAME

       gromacs - molecular dynamics simulation suite

DESCRIPTION

       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.

SYNOPSIS

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

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
         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
         mdrun_mpi   performs a sim across multiple CPUs or systems (in separate package)

Viewing trajectories

         ngmx        displays a trajectory
         trjconv     converts trajectories to e.g. pdb which can be viewed with e.g. rasmol
         g_nmtraj    generate a virtual trajectory from an eigenvector

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
         xpm2ps      converts XPM matrices to encapsulated postscript (or XPM)
         sigeps      convert c6/12 or c6/cn combinations to and from sigma/epsilon

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
         genrestr    generate topology include file with position restraints
         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
         xpm2ps      convert XPM (XPixelMap) file to postscript
         g_densmap   compute 2D number-density maps and generate plots
         g_sham      read/write xmgr and xvgr data sets
         g_spatial   calculates the spatial distribution function (more control than g_sdf)
         g_sdf       calculates the spatial distribution function (faster than g_spatial)

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

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  plot average static properties of polymers
         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_vanhove   compute Van Hove correlation function

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_principal calculate principal axes of inertion for a group of atoms
         g_rdf       calculates radial distribution functions
         g_sgangle   computes the angle and distance between two groups
         g_sorient   analyzes solvent orientation around solutes
         g_spol       analyze dipoles around a solute
         g_bundle    analyzes bundles of axes, e.g. helices
         g_disre     analyzes distance restraints
         g_clustsize calculate size distributions of atomic clusters
         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
         g_kinetics  calculate kinetic rate constants (experimental)

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
         g_current   calculate current autocorrelation function of system

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_helixorient calculate coordinates/directions of alpha-helix components
         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 essential-dynamics input file from g_covar output

Normal modes

         grompp      makes a run input file
         mdrun       finds a potential energy minimum
         mdrun       calculates the Hessian
         g_nmeig     diagonalizes the Hessian
         make_edi    generates essential-dynamics input file from g_nmeig analysis
         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

ADDITIONAL DOCUMENTATION

       Consult the manual at <http://www.gromacs.org/content/view/27/42/> 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/ .

REFERENCES

       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),
       <http://dx.doi.org/10.1021/ct700301q>

AUTHORS

       Current developers:

       David van der Spoel <spoel@gromacs.org>
       Berk Hess <hess@gromacs.org>
       Erik Lindahl <lindahl@gromacs.org>

       A full list of present and former contributors is available at
       <http://www.gromacs.org>

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

BUGS

       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.