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Man Pages


Manual Reference Pages  -  GROMACS (7)

NAME

gromacs - molecular dynamics simulation suite

CONTENTS

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.

Trajectory analysis




  gmx-gangle    Calculate angles
  gmx-distance  Calculate distances between pairs of positions
  gmx-freevolumeCalculate free volume
  gmx-sasa      Compute solvent accessible surface area
  gmx-select    Print general information about selections



Generating topologies and coordinates




  gmx-editconf  Edit the box and write subgroups
  gmx-protonate Protonate structures
  gmx-x2top     Generate a primitive topology from coordinates
  gmx-solvate   Solvate a system
  gmx-insert-moleculesInsert molecules into existing vacancies
  gmx-genconf   Multiply a conformation in ’random’ orientations
  gmx-genion    Generate monoatomic ions on energetically favorable positions
  gmx-genrestr  Generate position restraints or distance restraints for index groups
  gmx-pdb2gmx   Convert coordinate files to topology and FF-compliant coordinate files



Running a simulation




  gmx-grompp    Make a run input file
  gmx-mdrun     Perform a simulation, do a normal mode analysis or an energy minimization
  gmx-convert-tprMake a modifed run-input file



Viewing trajectories




  gmx-nmtraj    Generate a virtual oscillating trajectory from an eigenvector
  gmx-view      View a trajectory on an X-Windows terminal



Processing energies




  gmx-enemat    Extract an energy matrix from an energy file
  gmx-energy    Writes energies to xvg files and display averages
  gmx-mdrun     (Re)calculate energies for trajectory frames with -rerun



Converting files




  gmx-editconf  Convert and manipulates structure files
  gmx-eneconv   Convert energy files
  gmx-sigeps    Convert c6/12 or c6/cn combinations to and from sigma/epsilon
  gmx-trjcat    Concatenate trajectory files
  gmx-trjconv   Convert and manipulates trajectory files
  gmx-xpm2ps    Convert XPM (XPixelMap) matrices to postscript or XPM



Tools




  gmx-analyze   Analyze data sets
  gmx-dyndom    Interpolate and extrapolate structure rotations
  gmx-filter    Frequency filter trajectories, useful for making smooth movies
  gmx-lie       Estimate free energy from linear combinations
  gmx-morph     Interpolate linearly between conformations
  gmx-pme_error Estimate the error of using PME with a given input file
  gmx-sham      Compute free energies or other histograms from histograms
  gmx-spatial   Calculate the spatial distribution function
  gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-tune_pme  Time mdrun as a function of PME ranks to optimize settings
  gmx-wham      Perform weighted histogram analysis after umbrella sampling
  gmx-check     Check and compare files
  gmx-dump      Make binary files human readable
  gmx-make_ndx  Make index files
  gmx-mk_angndx Generate index files for ’gmx angle’
  gmx-trjorder  Order molecules according to their distance to a group
  gmx-xpm2ps    Convert XPM (XPixelMap) matrices to postscript or XPM



Distances between structures




  gmx-cluster   Cluster structures
  gmx-confrms   Fit two structures and calculates the RMSD
  gmx-rms       Calculate RMSDs with a reference structure and RMSD matrices
  gmx-rmsf      Calculate atomic fluctuations



Distances in structures over time




  gmx-mindist   Calculate the minimum distance between two groups
  gmx-mdmat     Calculate residue contact maps
  gmx-polystat  Calculate static properties of polymers
  gmx-rmsdist   Calculate atom pair distances averaged with power -2, -3 or -6



Mass distribution properties over time




  gmx-gyrate    Calculate the radius of gyration
  gmx-msd       Calculates mean square displacements
  gmx-polystat  Calculate static properties of polymers
  gmx-rdf       Calculate radial distribution functions
  gmx-rotacf    Calculate the rotational correlation function for molecules
  gmx-rotmat    Plot the rotation matrix for fitting to a reference structure
  gmx-sans      Compute small angle neutron scattering spectra
  gmx-saxs      Compute small angle X-ray scattering spectra
  gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-vanhove   Compute Van Hove displacement and correlation functions



Analyzing bonded interactions




  gmx-angle     Calculate distributions and correlations for angles and dihedrals
  gmx-mk_angndx Generate index files for ’gmx angle’



Structural properties




  gmx-anadock   Cluster structures from Autodock runs
  gmx-bundle    Analyze bundles of axes, e.g., helices
  gmx-clustsize Calculate size distributions of atomic clusters
  gmx-disre     Analyze distance restraints
  gmx-hbond     Compute and analyze hydrogen bonds
  gmx-order     Compute the order parameter per atom for carbon tails
  gmx-principal Calculate principal axes of inertia for a group of atoms
  gmx-rdf       Calculate radial distribution functions
  gmx-saltbr    Compute salt bridges
  gmx-sorient   Analyze solvent orientation around solutes
  gmx-spol      Analyze solvent dipole orientation and polarization around solutes



Kinetic properties




  gmx-bar       Calculate free energy difference estimates through Bennett’s acceptance ratio
  gmx-current   Calculate dielectric constants and current autocorrelation function
  gmx-dos       Analyze density of states and properties based on that
  gmx-dyecoupl  Extract dye dynamics from trajectories
  gmx-principal Calculate principal axes of inertia for a group of atoms
  gmx-tcaf      Calculate viscosities of liquids
  gmx-traj      Plot x, v, f, box, temperature and rotational energy from trajectories
  gmx-vanhove   Compute Van Hove displacement and correlation functions
  gmx-velacc    Calculate velocity autocorrelation functions



Electrostatic properties




  gmx-current   Calculate dielectric constants and current autocorrelation function
  gmx-dielectricCalculate frequency dependent dielectric constants
  gmx-dipoles   Compute the total dipole plus fluctuations
  gmx-potential Calculate the electrostatic potential across the box
  gmx-spol      Analyze solvent dipole orientation and polarization around solutes
  gmx-genion    Generate monoatomic ions on energetically favorable positions



Protein-specific analysis




  gmx-do_dssp   Assign secondary structure and calculate solvent accessible surface area
  gmx-chi       Calculate everything you want to know about chi and other dihedrals
  gmx-helix     Calculate basic properties of alpha helices
  gmx-helixorientCalculate local pitch/bending/rotation/orientation inside helices
  gmx-rama      Compute Ramachandran plots
  gmx-wheel     Plot helical wheels



Interfaces




  gmx-bundle    Analyze bundles of axes, e.g., helices
  gmx-density   Calculate the density of the system
  gmx-densmap   Calculate 2D planar or axial-radial density maps
  gmx-densorder Calculate surface fluctuations
  gmx-h2order   Compute the orientation of water molecules
  gmx-hydorder  Compute tetrahedrality parameters around a given atom
  gmx-order     Compute the order parameter per atom for carbon tails
  gmx-potential Calculate the electrostatic potential across the box



Covariance analysis




  gmx-anaeig    Analyze the eigenvectors
  gmx-covar     Calculate and diagonalize the covariance matrix
  gmx-make_edi  Generate input files for essential dynamics sampling



Normal modes




  gmx-anaeig    Analyze the normal modes
  gmx-nmeig     Diagonalize the Hessian for normal mode analysis
  gmx-nmtraj    Generate a virtual oscillating trajectory from an eigenvector
  gmx-nmens     Generate an ensemble of structures from the normal modes
  gmx-grompp    Make a run input file
  gmx-mdrun     Find a potential energy minimum and calculate the Hessian



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 is available in /usr/share/doc/gromacs/html/ .

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.
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