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gromacs

Langue: en

Version: 2008-10-12 (fedora - 01/12/10)

Section: 7 (Divers)

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
   g_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
   g_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, do a normal mode analysis or an energy minimization
   mdrun_mpi   performs a sim across multiple CPUs or systems
 
 

Viewing trajectories

   ngmx        displays a trajectory
   g_highway   X Window System gadget for highway simulations
   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)
   g_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
   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_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)
   g_select    selects groups of atoms based on flexible textual selections
   g_tune_pme  time mdrun as a function of PME nodes to optimize settings
 
 

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  calculates 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_polystat  calculates static properties of polymers
   g_rotacf    calculates the rotational correlation function for molecules
   g_rdf       calculates radial distribution functions
   g_rotmat    plots the rotation matrix for fitting to a reference structure
   g_vanhove   calculates Van Hove displacement 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_principal calculates axes of inertia for a group of atoms
   g_rdf       calculates radial distribution functions
   g_sdf       calculates solvent distribution functions
   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
   g_bundle    analyzes bundles of axes, e.g. helices
   g_disre     analyzes distance restraints
   g_clustsize calculate size distributions of atomic clusters
   g_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)
   g_bar       calculates free energy difference estimates through Bennett's acceptance ratio
   g_current   calculate current autocorrelation function of system
   g_vanhove   compute Van Hove correlation function
   g_principal calculate principal axes of inertion for a group of atoms
 
 

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
   g_spol       analyze dipoles around a solute
 
 

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
   g_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_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
   g_membed    embeds a protein into a lipid bilayer
 
 

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_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.
<Jayce> j'attaque Windows comme un virus
<Jayce> je le bouffe de l'intérieur puisque je ne peux pas le contrer
<Jayce> je le double
<Jayce> je gagne avec ou sans lui
-- Jayce - A genou ! --