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Carta.tech
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Packages
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gromacs-data
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283
- demux.1
- Convert xplor distance restraints to gromacs format
- do_dssp.1
- Assign secondary structure and calculate solvent accessible surface area
- do_dssp_d.1
- Assign secondary structure and calculate solvent accessible surface area
- editconf.1
- Convert and manipulates structure files
- editconf_d.1
- Convert and manipulates structure files
- eneconv.1
- Convert energy files
- eneconv_d.1
- Convert energy files
- g_anadock.1
- Cluster structures from autodock runs
- g_anadock_d.1
- Cluster structures from autodock runs
- g_anaeig.1
- Analyze eigenvectors/normal modes
- g_anaeig_d.1
- Analyze eigenvectors/normal modes
- g_analyze.1
- Analyze data sets
- g_analyze_d.1
- Analyze data sets
- g_angle.1
- Calculate distributions and correlations for angles and dihedrals
- g_angle_d.1
- Calculate distributions and correlations for angles and dihedrals
- g_bar.1
- Calculate free energy difference estimates through bennett's acceptance ratio
- g_bar_d.1
- Calculate free energy difference estimates through bennett's acceptance ratio
- g_bundle.1
- Analyze bundles of axes, e.g., helices
- g_bundle_d.1
- Analyze bundles of axes, e.g., helices
- g_chi.1
- Calculate everything you want to know about chi and other dihedrals
- g_chi_d.1
- Calculate everything you want to know about chi and other dihedrals
- g_cluster.1
- Cluster structures
- g_cluster_d.1
- Cluster structures
- g_clustsize.1
- Calculate size distributions of atomic clusters
- g_clustsize_d.1
- Calculate size distributions of atomic clusters
- g_confrms.1
- Fit two structures and calculates the rmsd
- g_confrms_d.1
- Fit two structures and calculates the rmsd
- g_covar.1
- Calculate and diagonalize the covariance matrix
- g_covar_d.1
- Calculate and diagonalize the covariance matrix
- g_current.1
- Calculate dielectric constants and current autocorrelation function
- g_current_d.1
- Calculate dielectric constants and current autocorrelation function
- g_density.1
- Calculate the density of the system
- g_density_d.1
- Calculate the density of the system
- g_densmap.1
- Calculate 2d planar or axial-radial density maps
- g_densmap_d.1
- Calculate 2d planar or axial-radial density maps
- g_densorder.1
- Calculate surface fluctuations
- g_densorder_d.1
- Calculate surface fluctuations
- g_dielectric.1
- Calculate frequency dependent dielectric constants
- g_dielectric_d.1
- Calculate frequency dependent dielectric constants
- g_dipoles.1
- Compute the total dipole plus fluctuations
- g_dipoles_d.1
- Compute the total dipole plus fluctuations
- g_disre.1
- Analyze distance restraints
- g_disre_d.1
- Analyze distance restraints
- g_dist.1
- Calculate distances between pairs of positions
- g_dist_d.1
- Calculate distances between pairs of positions
- g_dos.1
- Analyze density of states and properties based on that
- g_dos_d.1
- Analyze density of states and properties based on that
- g_dyecoupl.1
- Extract dye dynamics from trajectories
- g_dyecoupl_d.1
- Extract dye dynamics from trajectories
- g_dyndom.1
- Interpolate and extrapolate structure rotations
- g_dyndom_d.1
- Interpolate and extrapolate structure rotations
- g_enemat.1
- Extract an energy matrix from an energy file
- g_enemat_d.1
- Extract an energy matrix from an energy file
- g_energy.1
- Writes energies to xvg files and display averages
- g_energy_d.1
- Writes energies to xvg files and display averages
- g_filter.1
- Frequency filter trajectories, useful for making smooth movies
- g_filter_d.1
- Frequency filter trajectories, useful for making smooth movies
- g_gyrate.1
- Calculate the radius of gyration
- g_gyrate_d.1
- Calculate the radius of gyration
- g_h2order.1
- Compute the orientation of water molecules
- g_h2order_d.1
- Compute the orientation of water molecules
- g_hbond.1
- Compute and analyze hydrogen bonds
- g_hbond_d.1
- Compute and analyze hydrogen bonds
- g_helix.1
- Calculate basic properties of alpha helices
- g_helix_d.1
- Calculate basic properties of alpha helices
- g_helixorient.1
- Calculate local pitch/bending/rotation/orientation inside helices
- g_helixorient_d.1
- Calculate local pitch/bending/rotation/orientation inside helices
- g_hydorder.1
- Compute tetrahedrality parameters around a given atom
- g_hydorder_d.1
- Compute tetrahedrality parameters around a given atom
- g_lie.1
- Estimate free energy from linear combinations
- g_lie_d.1
- Estimate free energy from linear combinations
- g_mdmat.1
- Calculate residue contact maps
- g_mdmat_d.1
- Calculate residue contact maps
- g_mindist.1
- Calculate the minimum distance between two groups
- g_mindist_d.1
- Calculate the minimum distance between two groups
- g_morph.1
- Interpolate linearly between conformations
- g_morph_d.1
- Interpolate linearly between conformations
- g_msd.1
- Calculates mean square displacements
- g_msd_d.1
- Calculates mean square displacements
- g_nmeig.1
- Diagonalize the hessian for normal mode analysis
- g_nmeig_d.1
- Diagonalize the hessian for normal mode analysis
- g_nmens.1
- Generate an ensemble of structures from the normal modes
- g_nmens_d.1
- Generate an ensemble of structures from the normal modes
- g_nmtraj.1
- Generate a virtual oscillating trajectory from an eigenvector
- g_nmtraj_d.1
- Generate a virtual oscillating trajectory from an eigenvector
- g_options.1
- Utility program for generating gromacs documentation version 4.5.4
- g_options_d.1
- Utility program for generating gromacs documentation version 4.5.4
- g_order.1
- Compute the order parameter per atom for carbon tails
- g_order_d.1
- Compute the order parameter per atom for carbon tails
- g_pme_error.1
- Estimate the error of using pme with a given input file
- g_pme_error_d.1
- Estimate the error of using pme with a given input file
- g_polystat.1
- Calculate static properties of polymers
- g_polystat_d.1
- Calculate static properties of polymers
- g_potential.1
- Calculate the electrostatic potential across the box
- g_potential_d.1
- Calculate the electrostatic potential across the box
- g_principal.1
- Calculate principal axes of inertia for a group of atoms
- g_principal_d.1
- Calculate principal axes of inertia for a group of atoms
- g_protonate.1
- Protonate structures
- g_protonate_d.1
- Protonate structures
- g_rama.1
- Compute ramachandran plots
- g_rama_d.1
- Compute ramachandran plots
- g_rdf.1
- Calculate radial distribution functions
- g_rdf_d.1
- Calculate radial distribution functions
- g_rms.1
- Calculate rmsds with a reference structure and rmsd matrices
- g_rms_d.1
- Calculate rmsds with a reference structure and rmsd matrices
- g_rmsdist.1
- Calculate atom pair distances averaged with power -2, -3 or -6
- g_rmsdist_d.1
- Calculate atom pair distances averaged with power -2, -3 or -6
- g_rmsf.1
- Calculate atomic fluctuations
- g_rmsf_d.1
- Calculate atomic fluctuations
- g_rotacf.1
- Calculate the rotational correlation function for molecules
- g_rotacf_d.1
- Calculate the rotational correlation function for molecules
- g_rotmat.1
- Plot the rotation matrix for fitting to a reference structure
- g_rotmat_d.1
- Plot the rotation matrix for fitting to a reference structure
- g_saltbr.1
- Compute salt bridges
- g_saltbr_d.1
- Compute salt bridges
- g_sans.1
- Compute small angle neutron scattering spectra
- g_sans_d.1
- Compute small angle neutron scattering spectra
- g_sas.1
- Compute solvent accessible surface area
- g_sas_d.1
- Compute solvent accessible surface area
- g_saxs.1
- Compute small angle x-ray scattering spectra
- g_saxs_d.1
- Compute small angle x-ray scattering spectra
- g_select.1
- Print general information about selections
- g_select_d.1
- Print general information about selections
- g_sham.1
- Compute free energies or other histograms from histograms
- g_sham_d.1
- Compute free energies or other histograms from histograms
- g_sigeps.1
- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
- g_sigeps_d.1
- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
- g_sorient.1
- Analyze solvent orientation around solutes
- g_sorient_d.1
- Analyze solvent orientation around solutes
- g_spatial.1
- Calculate the spatial distribution function
- g_spatial_d.1
- Calculate the spatial distribution function
- g_spol.1
- Analyze solvent dipole orientation and polarization around solutes
- g_spol_d.1
- Analyze solvent dipole orientation and polarization around solutes
- g_tcaf.1
- Calculate viscosities of liquids
- g_tcaf_d.1
- Calculate viscosities of liquids
- g_traj.1
- Plot x, v, f, box, temperature and rotational energy from trajectories
- g_traj_d.1
- Plot x, v, f, box, temperature and rotational energy from trajectories
- g_tune_pme.1
- Time mdrun as a function of pme ranks to optimize settings
- g_tune_pme_d.1
- Time mdrun as a function of pme ranks to optimize settings
- g_vanhove.1
- Compute van hove displacement and correlation functions
- g_vanhove_d.1
- Compute van hove displacement and correlation functions
- g_velacc.1
- Calculate velocity autocorrelation functions
- g_velacc_d.1
- Calculate velocity autocorrelation functions
- g_view.1
- View a trajectory on an x-windows terminal
- g_view_d.1
- View a trajectory on an x-windows terminal
- g_wham.1
- Perform weighted histogram analysis after umbrella sampling
- g_wham_d.1
- Perform weighted histogram analysis after umbrella sampling
- g_wheel.1
- Plot helical wheels
- g_wheel_d.1
- Plot helical wheels
- g_x2top.1
- Generate a primitive topology from coordinates
- g_x2top_d.1
- Generate a primitive topology from coordinates
- genbox.1
- Solvate a system
- genbox_d.1
- Solvate a system
- genconf.1
- Multiply a conformation in 'random' orientations
- genconf_d.1
- Multiply a conformation in 'random' orientations
- genion.1
- Generate monoatomic ions on energetically favorable positions
- genion_d.1
- Generate monoatomic ions on energetically favorable positions
- genrestr.1
- Generate position restraints or distance restraints for index groups
- genrestr_d.1
- Generate position restraints or distance restraints for index groups
- gmx.1
- Master command for gromacs suite
- gmx-anadock.1
- Cluster structures from autodock runs
- gmx-anaeig.1
- Analyze eigenvectors/normal modes
- gmx-analyze.1
- Analyze data sets
- gmx-angle.1
- Calculate distributions and correlations for angles and dihedrals
- gmx-bar.1
- Calculate free energy difference estimates through bennett's acceptance ratio
- gmx-bundle.1
- Analyze bundles of axes, e.g., helices
- gmx-check.1
- Check and compare files
- gmx-chi.1
- Calculate everything you want to know about chi and other dihedrals
- gmx-cluster.1
- Cluster structures
- gmx-clustsize.1
- Calculate size distributions of atomic clusters
- gmx-confrms.1
- Fit two structures and calculates the rmsd
- gmx-convert-tpr.1
- Make a modifed run-input file
- gmx-covar.1
- Calculate and diagonalize the covariance matrix
- gmx-current.1
- Calculate dielectric constants and current autocorrelation function
- gmx-density.1
- Calculate the density of the system
- gmx-densmap.1
- Calculate 2d planar or axial-radial density maps
- gmx-densorder.1
- Calculate surface fluctuations
- gmx-dielectric.1
- Calculate frequency dependent dielectric constants
- gmx-dipoles.1
- Compute the total dipole plus fluctuations
- gmx-disre.1
- Analyze distance restraints
- gmx-distance.1
- Calculate distances between pairs of positions
- gmx-do_dssp.1
- Assign secondary structure and calculate solvent accessible surface area
- gmx-dos.1
- Analyze density of states and properties based on that
- gmx-dump.1
- Make binary files human readable
- gmx-dyecoupl.1
- Extract dye dynamics from trajectories
- gmx-dyndom.1
- Interpolate and extrapolate structure rotations
- gmx-editconf.1
- Convert and manipulates structure files
- gmx-eneconv.1
- Convert energy files
- gmx-enemat.1
- Extract an energy matrix from an energy file
- gmx-energy.1
- Writes energies to xvg files and display averages
- gmx-filter.1
- Frequency filter trajectories, useful for making smooth movies
- gmx-freevolume.1
- Calculate free volume
- gmx-gangle.1
- Calculate angles
- gmx-genconf.1
- Multiply a conformation in 'random' orientations
- gmx-genion.1
- Generate monoatomic ions on energetically favorable positions
- gmx-genrestr.1
- Generate position restraints or distance restraints for index groups
- gmx-grompp.1
- Make a run input file
- gmx-gyrate.1
- Calculate the radius of gyration
- gmx-h2order.1
- Compute the orientation of water molecules
- gmx-hbond.1
- Compute and analyze hydrogen bonds
- gmx-helix.1
- Calculate basic properties of alpha helices
- gmx-helixorient.1
- Calculate local pitch/bending/rotation/orientation inside helices
- gmx-help.1
- Print help information
- gmx-hydorder.1
- Compute tetrahedrality parameters around a given atom
- gmx-insert-molecules.1
- Insert molecules into existing vacancies
- gmx-lie.1
- Estimate free energy from linear combinations
- gmx-make_edi.1
- Generate input files for essential dynamics sampling
- gmx-make_ndx.1
- Make index files
- gmx-mdmat.1
- Calculate residue contact maps
- gmx-mdrun.1
- Perform a simulation, do a normal mode analysis or an energy minimization
- gmx-mindist.1
- Calculate the minimum distance between two groups
- gmx-mk_angndx.1
- Generate index files for 'gmx angle'
- gmx-morph.1
- Interpolate linearly between conformations
- gmx-msd.1
- Calculates mean square displacements
- gmx-nmeig.1
- Diagonalize the hessian for normal mode analysis
- gmx-nmens.1
- Generate an ensemble of structures from the normal modes
- gmx-nmtraj.1
- Generate a virtual oscillating trajectory from an eigenvector
- gmx-order.1
- Compute the order parameter per atom for carbon tails
- gmx-pdb2gmx.1
- Convert coordinate files to topology and ff-compliant coordinate files
- gmx-pme_error.1
- Estimate the error of using pme with a given input file
- gmx-polystat.1
- Calculate static properties of polymers
- gmx-potential.1
- Calculate the electrostatic potential across the box
- gmx-principal.1
- Calculate principal axes of inertia for a group of atoms
- gmx-protonate.1
- Protonate structures
- gmx-rama.1
- Compute ramachandran plots
- gmx-rdf.1
- Calculate radial distribution functions
- gmx-rms.1
- Calculate rmsds with a reference structure and rmsd matrices
- gmx-rmsdist.1
- Calculate atom pair distances averaged with power -2, -3 or -6
- gmx-rmsf.1
- Calculate atomic fluctuations
- gmx-rotacf.1
- Calculate the rotational correlation function for molecules
- gmx-rotmat.1
- Plot the rotation matrix for fitting to a reference structure
- gmx-saltbr.1
- Compute salt bridges
- gmx-sans.1
- Compute small angle neutron scattering spectra
- gmx-sasa.1
- Compute solvent accessible surface area
- gmx-saxs.1
- Compute small angle x-ray scattering spectra
- gmx-select.1
- Print general information about selections
- gmx-sham.1
- Compute free energies or other histograms from histograms
- gmx-sigeps.1
- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
- gmx-solvate.1
- Solvate a system
- gmx-sorient.1
- Analyze solvent orientation around solutes
- gmx-spatial.1
- Calculate the spatial distribution function
- gmx-spol.1
- Analyze solvent dipole orientation and polarization around solutes
- gmx-tcaf.1
- Calculate viscosities of liquids
- gmx-traj.1
- Plot x, v, f, box, temperature and rotational energy from trajectories
- gmx-trjcat.1
- Concatenate trajectory files
- gmx-trjconv.1
- Convert and manipulates trajectory files
- gmx-trjorder.1
- Order molecules according to their distance to a group
- gmx-tune_pme.1
- Time mdrun as a function of pme ranks to optimize settings
- gmx-vanhove.1
- Compute van hove displacement and correlation functions
- gmx-velacc.1
- Calculate velocity autocorrelation functions
- gmx-view.1
- View a trajectory on an x-windows terminal
- gmx-wham.1
- Perform weighted histogram analysis after umbrella sampling
- gmx-wheel.1
- Plot helical wheels
- gmx-x2top.1
- Generate a primitive topology from coordinates
- gmx-xpm2ps.1
- Convert xpm (xpixelmap) matrices to postscript or xpm
- gmx_d.1
- Master command for gromacs suite
- gmxcheck.1
- Check and compare files
- gmxcheck_d.1
- Check and compare files
- gmxdump.1
- Make binary files human readable
- gmxdump_d.1
- Make binary files human readable
- grompp.1
- Make a run input file
- grompp_d.1
- Make a run input file
- make_edi.1
- Generate input files for essential dynamics sampling
- make_edi_d.1
- Generate input files for essential dynamics sampling
- make_ndx.1
- Make index files
- make_ndx_d.1
- Make index files
- mdrun.1
- Perform a simulation, do a normal mode analysis or an energy minimization
- mdrun_d.1
- Perform a simulation, do a normal mode analysis or an energy minimization
- mk_angndx.1
- Generate index files for 'gmx angle'
- mk_angndx_d.1
- Generate index files for 'gmx angle'
- pdb2gmx.1
- Convert coordinate files to topology and ff-compliant coordinate files
- pdb2gmx_d.1
- Convert coordinate files to topology and ff-compliant coordinate files
- tpbconv.1
- Make a modifed run-input file
- tpbconv_d.1
- Make a modifed run-input file
- trjcat.1
- Concatenate trajectory files
- trjcat_d.1
- Concatenate trajectory files
- trjconv.1
- Convert and manipulates trajectory files
- trjconv_d.1
- Convert and manipulates trajectory files
- trjorder.1
- Order molecules according to their distance to a group
- trjorder_d.1
- Order molecules according to their distance to a group
- xplor2gmx.1
- Convert xplor distance restraints to gromacs format
- xpm2ps.1
- Convert xpm (xpixelmap) matrices to postscript or xpm
- xpm2ps_d.1
- Convert xpm (xpixelmap) matrices to postscript or xpm
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1
- gromacs.7
- Molecular dynamics simulation suite