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Packages

gromacsdata

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 axialradial density maps
 g_densmap_d.1
 Calculate 2d planar or axialradial 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 xray scattering spectra
 g_saxs_d.1
 Compute small angle xray 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 xwindows terminal
 g_view_d.1
 View a trajectory on an xwindows 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
 gmxanadock.1
 Cluster structures from autodock runs
 gmxanaeig.1
 Analyze eigenvectors/normal modes
 gmxanalyze.1
 Analyze data sets
 gmxangle.1
 Calculate distributions and correlations for angles and dihedrals
 gmxbar.1
 Calculate free energy difference estimates through bennett's acceptance ratio
 gmxbundle.1
 Analyze bundles of axes, e.g., helices
 gmxcheck.1
 Check and compare files
 gmxchi.1
 Calculate everything you want to know about chi and other dihedrals
 gmxcluster.1
 Cluster structures
 gmxclustsize.1
 Calculate size distributions of atomic clusters
 gmxconfrms.1
 Fit two structures and calculates the rmsd
 gmxconverttpr.1
 Make a modifed runinput file
 gmxcovar.1
 Calculate and diagonalize the covariance matrix
 gmxcurrent.1
 Calculate dielectric constants and current autocorrelation function
 gmxdensity.1
 Calculate the density of the system
 gmxdensmap.1
 Calculate 2d planar or axialradial density maps
 gmxdensorder.1
 Calculate surface fluctuations
 gmxdielectric.1
 Calculate frequency dependent dielectric constants
 gmxdipoles.1
 Compute the total dipole plus fluctuations
 gmxdisre.1
 Analyze distance restraints
 gmxdistance.1
 Calculate distances between pairs of positions
 gmxdo_dssp.1
 Assign secondary structure and calculate solvent accessible surface area
 gmxdos.1
 Analyze density of states and properties based on that
 gmxdump.1
 Make binary files human readable
 gmxdyecoupl.1
 Extract dye dynamics from trajectories
 gmxdyndom.1
 Interpolate and extrapolate structure rotations
 gmxeditconf.1
 Convert and manipulates structure files
 gmxeneconv.1
 Convert energy files
 gmxenemat.1
 Extract an energy matrix from an energy file
 gmxenergy.1
 Writes energies to xvg files and display averages
 gmxfilter.1
 Frequency filter trajectories, useful for making smooth movies
 gmxfreevolume.1
 Calculate free volume
 gmxgangle.1
 Calculate angles
 gmxgenconf.1
 Multiply a conformation in 'random' orientations
 gmxgenion.1
 Generate monoatomic ions on energetically favorable positions
 gmxgenrestr.1
 Generate position restraints or distance restraints for index groups
 gmxgrompp.1
 Make a run input file
 gmxgyrate.1
 Calculate the radius of gyration
 gmxh2order.1
 Compute the orientation of water molecules
 gmxhbond.1
 Compute and analyze hydrogen bonds
 gmxhelix.1
 Calculate basic properties of alpha helices
 gmxhelixorient.1
 Calculate local pitch/bending/rotation/orientation inside helices
 gmxhelp.1
 Print help information
 gmxhydorder.1
 Compute tetrahedrality parameters around a given atom
 gmxinsertmolecules.1
 Insert molecules into existing vacancies
 gmxlie.1
 Estimate free energy from linear combinations
 gmxmake_edi.1
 Generate input files for essential dynamics sampling
 gmxmake_ndx.1
 Make index files
 gmxmdmat.1
 Calculate residue contact maps
 gmxmdrun.1
 Perform a simulation, do a normal mode analysis or an energy minimization
 gmxmindist.1
 Calculate the minimum distance between two groups
 gmxmk_angndx.1
 Generate index files for 'gmx angle'
 gmxmorph.1
 Interpolate linearly between conformations
 gmxmsd.1
 Calculates mean square displacements
 gmxnmeig.1
 Diagonalize the hessian for normal mode analysis
 gmxnmens.1
 Generate an ensemble of structures from the normal modes
 gmxnmtraj.1
 Generate a virtual oscillating trajectory from an eigenvector
 gmxorder.1
 Compute the order parameter per atom for carbon tails
 gmxpdb2gmx.1
 Convert coordinate files to topology and ffcompliant coordinate files
 gmxpme_error.1
 Estimate the error of using pme with a given input file
 gmxpolystat.1
 Calculate static properties of polymers
 gmxpotential.1
 Calculate the electrostatic potential across the box
 gmxprincipal.1
 Calculate principal axes of inertia for a group of atoms
 gmxprotonate.1
 Protonate structures
 gmxrama.1
 Compute ramachandran plots
 gmxrdf.1
 Calculate radial distribution functions
 gmxrms.1
 Calculate rmsds with a reference structure and rmsd matrices
 gmxrmsdist.1
 Calculate atom pair distances averaged with power 2, 3 or 6
 gmxrmsf.1
 Calculate atomic fluctuations
 gmxrotacf.1
 Calculate the rotational correlation function for molecules
 gmxrotmat.1
 Plot the rotation matrix for fitting to a reference structure
 gmxsaltbr.1
 Compute salt bridges
 gmxsans.1
 Compute small angle neutron scattering spectra
 gmxsasa.1
 Compute solvent accessible surface area
 gmxsaxs.1
 Compute small angle xray scattering spectra
 gmxselect.1
 Print general information about selections
 gmxsham.1
 Compute free energies or other histograms from histograms
 gmxsigeps.1
 Convert c6/12 or c6/cn combinations to and from sigma/epsilon
 gmxsolvate.1
 Solvate a system
 gmxsorient.1
 Analyze solvent orientation around solutes
 gmxspatial.1
 Calculate the spatial distribution function
 gmxspol.1
 Analyze solvent dipole orientation and polarization around solutes
 gmxtcaf.1
 Calculate viscosities of liquids
 gmxtraj.1
 Plot x, v, f, box, temperature and rotational energy from trajectories
 gmxtrjcat.1
 Concatenate trajectory files
 gmxtrjconv.1
 Convert and manipulates trajectory files
 gmxtrjorder.1
 Order molecules according to their distance to a group
 gmxtune_pme.1
 Time mdrun as a function of pme ranks to optimize settings
 gmxvanhove.1
 Compute van hove displacement and correlation functions
 gmxvelacc.1
 Calculate velocity autocorrelation functions
 gmxview.1
 View a trajectory on an xwindows terminal
 gmxwham.1
 Perform weighted histogram analysis after umbrella sampling
 gmxwheel.1
 Plot helical wheels
 gmxx2top.1
 Generate a primitive topology from coordinates
 gmxxpm2ps.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 ffcompliant coordinate files
 pdb2gmx_d.1
 Convert coordinate files to topology and ffcompliant coordinate files
 tpbconv.1
 Make a modifed runinput file
 tpbconv_d.1
 Make a modifed runinput 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

1
 gromacs.7
 Molecular dynamics simulation suite