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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. .SH "SYNOPSIS" .IX Header "SYNOPSIS" .PP The following commands make up the GROMACS suite. Please refer to their individual man pages for further details. .Sh "Trajectory analysis" .IX Subsection "Trajectory analysis" .Vb .ta 16n \& gmx-gangle Calculate angles \& gmx-distance Calculate distances between pairs of positions \& gmx-freevolume Calculate free volume \& gmx-sasa Compute solvent accessible surface area \& gmx-select Print general information about selections .Ve .Sh "Generating topologies and coordinates" .IX Subsection "Generating topologies and coordinates" .Vb .ta 16n \& 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-molecules Insert 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 .Ve .Sh "Running a simulation" .IX Subsection "Running a simulation" .Vb .ta 16n \& gmx-grompp Make a run input file \& gmx-mdrun Perform a simulation, do a normal mode analysis or an energy minimization \& gmx-convert-tpr Make a modifed run-input file .Ve .Sh "Viewing trajectories" .IX Subsection "Viewing trajectories" .Vb .ta 16n \& gmx-nmtraj Generate a virtual oscillating trajectory from an eigenvector \& gmx-view View a trajectory on an X-Windows terminal .Ve .Sh "Processing energies" .IX Subsection "Processing energies" .Vb .ta 16n \& 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 .Ve .Sh "Converting files" .IX Subsection "Converting files" .Vb .ta 16n \& 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 .Ve .Sh "Tools" .IX Subsection "Tools" .Vb .ta 16n \& 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 .Ve .Sh "Distances between structures" .IX Subsection "Distances between structures" .Vb .ta 16n \& 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 .Ve .Sh "Distances in structures over time" .IX Subsection "Distances in structures over time" .Vb .ta 16n \& 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 .Ve .Sh "Mass distribution properties over time" .IX Subsection "Mass distribution properties over time" .Vb .ta 16n \& 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 .Ve .Sh "Analyzing bonded interactions" .IX Subsection "Analyzing bonded interactions" .Vb .ta 16n \& gmx-angle Calculate distributions and correlations for angles and dihedrals \& gmx-mk_angndx Generate index files for 'gmx angle' .Ve .Sh "Structural properties" .IX Subsection "Structural properties" .Vb .ta 16n \& 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 .Ve .Sh "Kinetic properties" .IX Subsection "Kinetic properties" .Vb .ta 16n \& 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 .Ve .Sh "Electrostatic properties" .IX Subsection "Electrostatic properties" .Vb .ta 16n \& gmx-current Calculate dielectric constants and current autocorrelation function \& gmx-dielectric Calculate 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 .Ve .Sh "Protein-specific analysis" .IX Subsection "Protein-specific analysis" .Vb .ta 16n \& 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-helixorient Calculate local pitch/bending/rotation/orientation inside helices \& gmx-rama Compute Ramachandran plots \& gmx-wheel Plot helical wheels .Ve .Sh "Interfaces" .IX Subsection "Interfaces" .Vb .ta 16n \& 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 .Ve .Sh "Covariance analysis" .IX Subsection "Covariance analysis" .Vb .ta 16n \& gmx-anaeig Analyze the eigenvectors \& gmx-covar Calculate and diagonalize the covariance matrix \& gmx-make_edi Generate input files for essential dynamics sampling .Ve .Sh "Normal modes" .IX Subsection "Normal modes" .Vb .ta 16n \& 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 .Ve .PP .SH "ADDITIONAL DOCUMENTATION" .IX Header "ADDITIONAL DOCUMENTATION" Consult the manual at <\fIhttp://www.gromacs.org/content/view/27/42/\fR> for an introduction to molecular dynamics in general and GROMACS in particular, as well as an overview of the individual programs. .PP The shorter HTML reference is available in \fB/usr/share/doc/gromacs/html/\fR . .SH "REFERENCES" .IX Header "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: .PP H.J.C. Berendsen, D. van der Spoel and R. van Drunen. \fBGROMACS: A message-passing parallel molecular dynamics implementation\fR. Comp. Phys. Comm. \fI91\fR, 43-56 (1995) .PP Erik Lindahl, Berk Hess and David van der Spoel. \fBGROMACS 3.0: A package for molecular simulation and trajectory analysis\fR. J. Mol. Mod. \fI7\fR, 306-317 (2001) .PP B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. \fBGROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation\fR. J. Chem. Theory Comput. \fI4\fR, 3, 435-447 (2008), <\fIhttp://dx.doi.org/10.1021/ct700301q\fR> .SH "AUTHORS" .IX Header "AUTHORS" Current developers: .PP David van der Spoel .br Berk Hess .br Erik Lindahl .PP A full list of present and former contributors is available at .PP This manual page is largely based on the GROMACS online reference, and was prepared in this format by Nicholas Breen . .SH "BUGS" .IX Header "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.