/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
private:
- void printMessage() const
+ static void printMessage()
{
std::fprintf(stderr,
"This tool is no longer present in GROMACS. Please see\n"
" "
- "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/"
- "user-guide/cmdline.html#command-changes\n"
+ "https://manual.gromacs.org/current/user-guide/"
+ "cmdline.html#command-changes-between-versions\n"
"for ideas how to perform the same tasks with the "
"new tools.\n");
}
gmx::ICommandLineOptionsModule::registerModuleFactory(
manager, gmx::DumpInfo::name, gmx::DumpInfo::shortDescription, &gmx::DumpInfo::create);
registerModule(manager, &gmx_grompp, "grompp", "Make a run input file");
- registerModule(manager, &gmx_convert_tpr, "convert-tpr", "Make a modifed run-input file");
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::ConvertTprInfo::name,
+ gmx::ConvertTprInfo::shortDescription,
+ &gmx::ConvertTprInfo::create);
registerObsoleteTool(manager, "tpbconv");
registerModule(manager, &gmx_x2top, "x2top", "Generate a primitive topology from coordinates");
registerModuleNoNice(
- manager, &gmx::gmx_mdrun, "mdrun",
+ manager,
+ &gmx::gmx_mdrun,
+ "mdrun",
"Perform a simulation, do a normal mode analysis or an energy minimization");
- gmx::ICommandLineOptionsModule::registerModuleFactory(
- manager, gmx::NonbondedBenchmarkInfo::name,
- gmx::NonbondedBenchmarkInfo::shortDescription, &gmx::NonbondedBenchmarkInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::NonbondedBenchmarkInfo::name,
+ gmx::NonbondedBenchmarkInfo::shortDescription,
+ &gmx::NonbondedBenchmarkInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::InsertMoleculesInfo::name(),
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::InsertMoleculesInfo::name(),
gmx::InsertMoleculesInfo::shortDescription(),
&gmx::InsertMoleculesInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::ReportMethodsInfo::name,
+ gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
+ gmx::ReportMethodsInfo::name,
gmx::ReportMethodsInfo::shortDescription,
&gmx::ReportMethodsInfo::create);
- gmx::ICommandLineOptionsModule::registerModuleFactory(manager, gmx::pdb2gmxInfo::name,
- gmx::pdb2gmxInfo::shortDescription,
- &gmx::pdb2gmxInfo::create);
+ gmx::ICommandLineOptionsModule::registerModuleFactory(
+ manager, gmx::pdb2gmxInfo::name, gmx::pdb2gmxInfo::shortDescription, &gmx::pdb2gmxInfo::create);
// Modules from gmx_ana.h.
- registerModule(manager, &gmx_do_dssp, "do_dssp",
+ registerModule(manager,
+ &gmx_do_dssp,
+ "do_dssp",
"Assign secondary structure and calculate solvent accessible surface area");
registerModule(manager, &gmx_editconf, "editconf", "Convert and manipulates structure files");
registerModule(manager, &gmx_eneconv, "eneconv", "Convert energy files");
registerModule(manager, &gmx_solvate, "solvate", "Solvate a system");
registerObsoleteTool(manager, "genbox");
- registerModule(manager, &gmx_genconf, "genconf",
- "Multiply a conformation in 'random' orientations");
- registerModule(manager, &gmx_genion, "genion",
+ registerModule(
+ manager, &gmx_genconf, "genconf", "Multiply a conformation in 'random' orientations");
+ registerModule(manager,
+ &gmx_genion,
+ "genion",
"Generate monoatomic ions on energetically favorable positions");
- registerModule(manager, &gmx_genrestr, "genrestr",
+ registerModule(manager,
+ &gmx_genrestr,
+ "genrestr",
"Generate position restraints or distance restraints for index groups");
- registerModule(manager, &gmx_make_edi, "make_edi",
+ registerModule(manager,
+ &gmx_make_edi,
+ "make_edi",
"Generate input files for essential dynamics sampling");
registerModule(manager, &gmx_make_ndx, "make_ndx", "Make index files");
registerModule(manager, &gmx_mk_angndx, "mk_angndx", "Generate index files for 'gmx angle'");
registerModule(manager, &gmx_trjcat, "trjcat", "Concatenate trajectory files");
registerModule(manager, &gmx_trjconv, "trjconv", "Convert and manipulates trajectory files");
- registerModule(manager, &gmx_trjorder, "trjorder",
+ registerModule(manager,
+ &gmx_trjorder,
+ "trjorder",
"Order molecules according to their distance to a group");
- registerModule(manager, &gmx_xpm2ps, "xpm2ps",
- "Convert XPM (XPixelMap) matrices to postscript or XPM");
+ registerModule(
+ manager, &gmx_xpm2ps, "xpm2ps", "Convert XPM (XPixelMap) matrices to postscript or XPM");
registerModule(manager, &gmx_anaeig, "anaeig", "Analyze eigenvectors/normal modes");
registerModule(manager, &gmx_analyze, "analyze", "Analyze data sets");
- registerModule(manager, &gmx_g_angle, "angle",
+ registerModule(manager,
+ &gmx_g_angle,
+ "angle",
"Calculate distributions and correlations for angles and dihedrals");
- registerModule(manager, &gmx_awh, "awh",
- "Extract data from an accelerated weight histogram (AWH) run");
- registerModule(manager, &gmx_bar, "bar",
+ registerModule(
+ manager, &gmx_awh, "awh", "Extract data from an accelerated weight histogram (AWH) run");
+ registerModule(manager,
+ &gmx_bar,
+ "bar",
"Calculate free energy difference estimates through Bennett's acceptance ratio");
registerObsoleteTool(manager, "bond");
registerObsoleteTool(manager, "dist");
registerObsoleteTool(manager, "sgangle");
registerModule(manager, &gmx_bundle, "bundle", "Analyze bundles of axes, e.g., helices");
- registerModule(manager, &gmx_chi, "chi",
+ registerModule(manager,
+ &gmx_chi,
+ "chi",
"Calculate everything you want to know about chi and other dihedrals");
registerModule(manager, &gmx_cluster, "cluster", "Cluster structures");
- registerModule(manager, &gmx_clustsize, "clustsize",
- "Calculate size distributions of atomic clusters");
+ registerModule(
+ manager, &gmx_clustsize, "clustsize", "Calculate size distributions of atomic clusters");
registerModule(manager, &gmx_confrms, "confrms", "Fit two structures and calculates the RMSD");
registerModule(manager, &gmx_covar, "covar", "Calculate and diagonalize the covariance matrix");
- registerModule(manager, &gmx_current, "current",
+ registerModule(manager,
+ &gmx_current,
+ "current",
"Calculate dielectric constants and current autocorrelation function");
registerModule(manager, &gmx_density, "density", "Calculate the density of the system");
- registerModule(manager, &gmx_densmap, "densmap",
- "Calculate 2D planar or axial-radial density maps");
+ registerModule(
+ manager, &gmx_densmap, "densmap", "Calculate 2D planar or axial-radial density maps");
registerModule(manager, &gmx_densorder, "densorder", "Calculate surface fluctuations");
- registerModule(manager, &gmx_dielectric, "dielectric",
+ registerModule(manager,
+ &gmx_dielectric,
+ "dielectric",
"Calculate frequency dependent dielectric constants");
registerModule(manager, &gmx_dipoles, "dipoles", "Compute the total dipole plus fluctuations");
registerModule(manager, &gmx_disre, "disre", "Analyze distance restraints");
- registerModule(manager, &gmx_dos, "dos",
- "Analyze density of states and properties based on that");
+ registerModule(
+ manager, &gmx_dos, "dos", "Analyze density of states and properties based on that");
registerModule(manager, &gmx_dyecoupl, "dyecoupl", "Extract dye dynamics from trajectories");
registerModule(manager, &gmx_enemat, "enemat", "Extract an energy matrix from an energy file");
- registerModule(manager, &gmx_energy, "energy",
- "Writes energies to xvg files and display averages");
- registerModule(manager, &gmx_filter, "filter",
+ registerModule(
+ manager, &gmx_energy, "energy", "Writes energies to xvg files and display averages");
+ registerModule(manager,
+ &gmx_filter,
+ "filter",
"Frequency filter trajectories, useful for making smooth movies");
registerModule(manager, &gmx_gyrate, "gyrate", "Calculate the radius of gyration");
registerModule(manager, &gmx_h2order, "h2order", "Compute the orientation of water molecules");
registerModule(manager, &gmx_hbond, "hbond", "Compute and analyze hydrogen bonds");
registerModule(manager, &gmx_helix, "helix", "Calculate basic properties of alpha helices");
- registerModule(manager, &gmx_helixorient, "helixorient",
+ registerModule(manager,
+ &gmx_helixorient,
+ "helixorient",
"Calculate local pitch/bending/rotation/orientation inside helices");
- registerModule(manager, &gmx_hydorder, "hydorder",
+ registerModule(manager,
+ &gmx_hydorder,
+ "hydorder",
"Compute tetrahedrality parameters around a given atom");
registerModule(manager, &gmx_lie, "lie", "Estimate free energy from linear combinations");
registerModule(manager, &gmx_mdmat, "mdmat", "Calculate residue contact maps");
- registerModule(manager, &gmx_mindist, "mindist",
- "Calculate the minimum distance between two groups");
- registerModule(manager, &gmx_msd, "msd", "Calculates mean square displacements");
+ registerModule(
+ manager, &gmx_mindist, "mindist", "Calculate the minimum distance between two groups");
registerModule(manager, &gmx_nmeig, "nmeig", "Diagonalize the Hessian for normal mode analysis");
- registerModule(manager, &gmx_nmens, "nmens",
+ registerModule(manager,
+ &gmx_nmens,
+ "nmens",
"Generate an ensemble of structures from the normal modes");
- registerModule(manager, &gmx_nmr, "nmr",
+ registerModule(manager,
+ &gmx_nmr,
+ "nmr",
"Analyze nuclear magnetic resonance properties from an energy file");
- registerModule(manager, &gmx_nmtraj, "nmtraj",
+ registerModule(manager,
+ &gmx_nmtraj,
+ "nmtraj",
"Generate a virtual oscillating trajectory from an eigenvector");
- registerModule(manager, &gmx_order, "order",
- "Compute the order parameter per atom for carbon tails");
- registerModule(manager, &gmx_pme_error, "pme_error",
+ registerModule(
+ manager, &gmx_order, "order", "Compute the order parameter per atom for carbon tails");
+ registerModule(manager,
+ &gmx_pme_error,
+ "pme_error",
"Estimate the error of using PME with a given input file");
registerModule(manager, &gmx_polystat, "polystat", "Calculate static properties of polymers");
- registerModule(manager, &gmx_potential, "potential",
+ registerModule(manager,
+ &gmx_potential,
+ "potential",
"Calculate the electrostatic potential across the box");
- registerModule(manager, &gmx_principal, "principal",
+ registerModule(manager,
+ &gmx_principal,
+ "principal",
"Calculate principal axes of inertia for a group of atoms");
registerModule(manager, &gmx_rama, "rama", "Compute Ramachandran plots");
- registerModule(manager, &gmx_rms, "rms",
+ registerModule(manager,
+ &gmx_rms,
+ "rms",
"Calculate RMSDs with a reference structure and RMSD matrices");
- registerModule(manager, &gmx_rmsdist, "rmsdist",
+ registerModule(manager,
+ &gmx_rmsdist,
+ "rmsdist",
"Calculate atom pair distances averaged with power -2, -3 or -6");
registerModule(manager, &gmx_rmsf, "rmsf", "Calculate atomic fluctuations");
- registerModule(manager, &gmx_rotacf, "rotacf",
+ registerModule(manager,
+ &gmx_rotacf,
+ "rotacf",
"Calculate the rotational correlation function for molecules");
- registerModule(manager, &gmx_rotmat, "rotmat",
+ registerModule(manager,
+ &gmx_rotmat,
+ "rotmat",
"Plot the rotation matrix for fitting to a reference structure");
registerModule(manager, &gmx_saltbr, "saltbr", "Compute salt bridges");
registerModule(manager, &gmx_sans, "sans", "Compute small angle neutron scattering spectra");
registerModule(manager, &gmx_saxs, "saxs", "Compute small angle X-ray scattering spectra");
- registerModule(manager, &gmx_sham, "sham",
- "Compute free energies or other histograms from histograms");
- registerModule(manager, &gmx_sigeps, "sigeps",
+ registerModule(
+ manager, &gmx_sham, "sham", "Compute free energies or other histograms from histograms");
+ registerModule(manager,
+ &gmx_sigeps,
+ "sigeps",
"Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
registerModule(manager, &gmx_sorient, "sorient", "Analyze solvent orientation around solutes");
registerModule(manager, &gmx_spatial, "spatial", "Calculate the spatial distribution function");
- registerModule(manager, &gmx_spol, "spol",
+ registerModule(manager,
+ &gmx_spol,
+ "spol",
"Analyze solvent dipole orientation and polarization around solutes");
registerModule(manager, &gmx_tcaf, "tcaf", "Calculate viscosities of liquids");
- registerModule(manager, &gmx_traj, "traj",
+ registerModule(manager,
+ &gmx_traj,
+ "traj",
"Plot x, v, f, box, temperature and rotational energy from trajectories");
- registerModule(manager, &gmx_tune_pme, "tune_pme",
+ registerModule(manager,
+ &gmx_tune_pme,
+ "tune_pme",
"Time mdrun as a function of PME ranks to optimize settings");
- registerModule(manager, &gmx_vanhove, "vanhove",
+ registerModule(manager,
+ &gmx_vanhove,
+ "vanhove",
"Compute Van Hove displacement and correlation functions");
registerModule(manager, &gmx_velacc, "velacc", "Calculate velocity autocorrelation functions");
- registerModule(manager, &gmx_wham, "wham",
+ registerModule(manager,
+ &gmx_wham,
+ "wham",
"Perform weighted histogram analysis after umbrella sampling");
registerModule(manager, &gmx_wheel, "wheel", "Plot helical wheels");
registerModuleNoNice(manager, &gmx_view, "view", "View a trajectory on an X-Windows terminal");
gmx::CommandLineModuleGroup group =
manager->addModuleGroup("Mass distribution properties over time");
group.addModule("gyrate");
- group.addModule("msd");
group.addModule("polystat");
group.addModule("rdf");
group.addModule("rotacf");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff