src/programs/legacymodules.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
   5  * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36 /*! \internal \brief
  37  * Registers command-line modules for pre-5.0 binaries.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  */
  41 #include "gmxpre.h"
  42
  43 #include "legacymodules.h"
  44
  45 #include <cstdio>
  46
  47 #include "gromacs/commandline/cmdlinemodule.h"
  48 #include "gromacs/commandline/cmdlinemodulemanager.h"
  49 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  50 #include "gromacs/gmxana/gmx_ana.h"
  51 #include "gromacs/gmxpreprocess/editconf.h"
  52 #include "gromacs/gmxpreprocess/genconf.h"
  53 #include "gromacs/gmxpreprocess/genion.h"
  54 #include "gromacs/gmxpreprocess/genrestr.h"
  55 #include "gromacs/gmxpreprocess/grompp.h"
  56 #include "gromacs/gmxpreprocess/insert_molecules.h"
  57 #include "gromacs/gmxpreprocess/pdb2gmx.h"
  58 #include "gromacs/gmxpreprocess/solvate.h"
  59 #include "gromacs/gmxpreprocess/x2top.h"
  60 #include "gromacs/tools/check.h"
  61 #include "gromacs/tools/convert_tpr.h"
  62 #include "gromacs/tools/dump.h"
  63 #include "gromacs/tools/eneconv.h"
  64 #include "gromacs/tools/make_ndx.h"
  65 #include "gromacs/tools/mk_angndx.h"
  66 #include "gromacs/tools/pme_error.h"
  67 #include "gromacs/tools/report_methods.h"
  68 #include "gromacs/tools/trjcat.h"
  69 #include "gromacs/tools/trjconv.h"
  70 #include "gromacs/tools/tune_pme.h"
  71
  72 #include "mdrun/mdrun_main.h"
  73 #include "mdrun/nonbonded_bench.h"
  74 #include "view/view.h"
  75
  76 namespace
  77 {
  78
  79 /*! \brief
  80  * Command line module that provides information about obsolescence.
  81  *
  82  * Prints a message directing the user to a wiki page describing replacement
  83  * options.
  84  */
  85 class ObsoleteToolModule : public gmx::ICommandLineModule
  86 {
  87 public:
  88     //! Creates an obsolete tool module for a tool with the given name.
  89     explicit ObsoleteToolModule(const char* name) : name_(name) {}
  90
  91     const char* name() const override { return name_; }
  92     const char* shortDescription() const override { return nullptr; }
  93
  94     void init(gmx::CommandLineModuleSettings* /*settings*/) override {}
  95     int  run(int /*argc*/, char* /*argv*/[]) override
  96     {
  97         printMessage();
  98         return 0;
  99     }
 100     void writeHelp(const gmx::CommandLineHelpContext& /*context*/) const override
 101     {
 102         printMessage();
 103     }
 104
 105 private:
 106     static void printMessage()
 107     {
 108         std::fprintf(stderr,
 109                      "This tool is no longer present in GROMACS. Please see\n"
 110                      "  "
 111                      "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/"
 112                      "user-guide/cmdline.html#command-changes\n"
 113                      "for ideas how to perform the same tasks with the "
 114                      "new tools.\n");
 115     }
 116
 117     const char* name_;
 118 };
 119
 120 //! Initializer for a module that defaults to nice level zero.
 121 void initSettingsNoNice(gmx::CommandLineModuleSettings* settings)
 122 {
 123     settings->setDefaultNiceLevel(0);
 124 }
 125
 126 /*! \brief
 127  * Convenience function for creating and registering a module.
 128  *
 129  * \param[in] manager          Module manager to which to register the module.
 130  * \param[in] mainFunction     Main function to wrap.
 131  * \param[in] name             Name for the new module.
 132  * \param[in] shortDescription One-line description for the new module.
 133  */
 134 void registerModule(gmx::CommandLineModuleManager*               manager,
 135                     gmx::CommandLineModuleManager::CMainFunction mainFunction,
 136                     const char*                                  name,
 137                     const char*                                  shortDescription)
 138 {
 139     manager->addModuleCMain(name, shortDescription, mainFunction);
 140 }
 141
 142 /*! \brief
 143  * Convenience function for creating and registering a module that defaults to
 144  * -nice 0.
 145  *
 146  * \param[in] manager          Module manager to which to register the module.
 147  * \param[in] mainFunction     Main function to wrap.
 148  * \param[in] name             Name for the new module.
 149  * \param[in] shortDescription One-line description for the new module.
 150  */
 151 void registerModuleNoNice(gmx::CommandLineModuleManager*               manager,
 152                           gmx::CommandLineModuleManager::CMainFunction mainFunction,
 153                           const char*                                  name,
 154                           const char*                                  shortDescription)
 155 {
 156     manager->addModuleCMainWithSettings(name, shortDescription, mainFunction, &initSettingsNoNice);
 157 }
 158
 159 /*! \brief
 160  * Convenience function for registering a module for an obsolete tool.
 161  *
 162  * \param[in] manager          Module manager to which to register the module.
 163  * \param[in] name             Name for the obsolete tool.
 164  */
 165 void registerObsoleteTool(gmx::CommandLineModuleManager* manager, const char* name)
 166 {
 167     gmx::CommandLineModulePointer module(new ObsoleteToolModule(name));
 168     manager->addModule(std::move(module));
 169 }
 170
 171 } // namespace
 172
 173 void registerLegacyModules(gmx::CommandLineModuleManager* manager)
 174 {
 175     registerModule(manager, &gmx_check, "check", "Check and compare files");
 176     gmx::ICommandLineOptionsModule::registerModuleFactory(
 177             manager, gmx::DumpInfo::name, gmx::DumpInfo::shortDescription, &gmx::DumpInfo::create);
 178     registerModule(manager, &gmx_grompp, "grompp", "Make a run input file");
 179     gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
 180                                                           gmx::ConvertTprInfo::name,
 181                                                           gmx::ConvertTprInfo::shortDescription,
 182                                                           &gmx::ConvertTprInfo::create);
 183     registerObsoleteTool(manager, "tpbconv");
 184     registerModule(manager, &gmx_x2top, "x2top", "Generate a primitive topology from coordinates");
 185
 186     registerModuleNoNice(
 187             manager,
 188             &gmx::gmx_mdrun,
 189             "mdrun",
 190             "Perform a simulation, do a normal mode analysis or an energy minimization");
 191
 192     gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
 193                                                           gmx::NonbondedBenchmarkInfo::name,
 194                                                           gmx::NonbondedBenchmarkInfo::shortDescription,
 195                                                           &gmx::NonbondedBenchmarkInfo::create);
 196
 197     gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
 198                                                           gmx::InsertMoleculesInfo::name(),
 199                                                           gmx::InsertMoleculesInfo::shortDescription(),
 200                                                           &gmx::InsertMoleculesInfo::create);
 201
 202     gmx::ICommandLineOptionsModule::registerModuleFactory(manager,
 203                                                           gmx::ReportMethodsInfo::name,
 204                                                           gmx::ReportMethodsInfo::shortDescription,
 205                                                           &gmx::ReportMethodsInfo::create);
 206
 207     gmx::ICommandLineOptionsModule::registerModuleFactory(
 208             manager, gmx::pdb2gmxInfo::name, gmx::pdb2gmxInfo::shortDescription, &gmx::pdb2gmxInfo::create);
 209
 210     // Modules from gmx_ana.h.
 211     registerModule(manager,
 212                    &gmx_do_dssp,
 213                    "do_dssp",
 214                    "Assign secondary structure and calculate solvent accessible surface area");
 215     registerModule(manager, &gmx_editconf, "editconf", "Convert and manipulates structure files");
 216     registerModule(manager, &gmx_eneconv, "eneconv", "Convert energy files");
 217     registerModule(manager, &gmx_solvate, "solvate", "Solvate a system");
 218     registerObsoleteTool(manager, "genbox");
 219     registerModule(
 220             manager, &gmx_genconf, "genconf", "Multiply a conformation in 'random' orientations");
 221     registerModule(manager,
 222                    &gmx_genion,
 223                    "genion",
 224                    "Generate monoatomic ions on energetically favorable positions");
 225     registerModule(manager,
 226                    &gmx_genrestr,
 227                    "genrestr",
 228                    "Generate position restraints or distance restraints for index groups");
 229     registerModule(manager,
 230                    &gmx_make_edi,
 231                    "make_edi",
 232                    "Generate input files for essential dynamics sampling");
 233     registerModule(manager, &gmx_make_ndx, "make_ndx", "Make index files");
 234     registerModule(manager, &gmx_mk_angndx, "mk_angndx", "Generate index files for 'gmx angle'");
 235     registerModule(manager, &gmx_trjcat, "trjcat", "Concatenate trajectory files");
 236     registerModule(manager, &gmx_trjconv, "trjconv", "Convert and manipulates trajectory files");
 237     registerModule(manager,
 238                    &gmx_trjorder,
 239                    "trjorder",
 240                    "Order molecules according to their distance to a group");
 241     registerModule(
 242             manager, &gmx_xpm2ps, "xpm2ps", "Convert XPM (XPixelMap) matrices to postscript or XPM");
 243
 244     registerModule(manager, &gmx_anaeig, "anaeig", "Analyze eigenvectors/normal modes");
 245     registerModule(manager, &gmx_analyze, "analyze", "Analyze data sets");
 246     registerModule(manager,
 247                    &gmx_g_angle,
 248                    "angle",
 249                    "Calculate distributions and correlations for angles and dihedrals");
 250     registerModule(
 251             manager, &gmx_awh, "awh", "Extract data from an accelerated weight histogram (AWH) run");
 252     registerModule(manager,
 253                    &gmx_bar,
 254                    "bar",
 255                    "Calculate free energy difference estimates through Bennett's acceptance ratio");
 256     registerObsoleteTool(manager, "bond");
 257     registerObsoleteTool(manager, "dist");
 258     registerObsoleteTool(manager, "sas");
 259     registerObsoleteTool(manager, "sgangle");
 260
 261     registerModule(manager, &gmx_bundle, "bundle", "Analyze bundles of axes, e.g., helices");
 262     registerModule(manager,
 263                    &gmx_chi,
 264                    "chi",
 265                    "Calculate everything you want to know about chi and other dihedrals");
 266     registerModule(manager, &gmx_cluster, "cluster", "Cluster structures");
 267     registerModule(
 268             manager, &gmx_clustsize, "clustsize", "Calculate size distributions of atomic clusters");
 269     registerModule(manager, &gmx_confrms, "confrms", "Fit two structures and calculates the RMSD");
 270     registerModule(manager, &gmx_covar, "covar", "Calculate and diagonalize the covariance matrix");
 271     registerModule(manager,
 272                    &gmx_current,
 273                    "current",
 274                    "Calculate dielectric constants and current autocorrelation function");
 275     registerModule(manager, &gmx_density, "density", "Calculate the density of the system");
 276     registerModule(
 277             manager, &gmx_densmap, "densmap", "Calculate 2D planar or axial-radial density maps");
 278     registerModule(manager, &gmx_densorder, "densorder", "Calculate surface fluctuations");
 279     registerModule(manager,
 280                    &gmx_dielectric,
 281                    "dielectric",
 282                    "Calculate frequency dependent dielectric constants");
 283     registerModule(manager, &gmx_dipoles, "dipoles", "Compute the total dipole plus fluctuations");
 284     registerModule(manager, &gmx_disre, "disre", "Analyze distance restraints");
 285     registerModule(
 286             manager, &gmx_dos, "dos", "Analyze density of states and properties based on that");
 287     registerModule(manager, &gmx_dyecoupl, "dyecoupl", "Extract dye dynamics from trajectories");
 288     registerModule(manager, &gmx_enemat, "enemat", "Extract an energy matrix from an energy file");
 289     registerModule(
 290             manager, &gmx_energy, "energy", "Writes energies to xvg files and display averages");
 291     registerModule(manager,
 292                    &gmx_filter,
 293                    "filter",
 294                    "Frequency filter trajectories, useful for making smooth movies");
 295     registerModule(manager, &gmx_gyrate, "gyrate", "Calculate the radius of gyration");
 296     registerModule(manager, &gmx_h2order, "h2order", "Compute the orientation of water molecules");
 297     registerModule(manager, &gmx_hbond, "hbond", "Compute and analyze hydrogen bonds");
 298     registerModule(manager, &gmx_helix, "helix", "Calculate basic properties of alpha helices");
 299     registerModule(manager,
 300                    &gmx_helixorient,
 301                    "helixorient",
 302                    "Calculate local pitch/bending/rotation/orientation inside helices");
 303     registerModule(manager,
 304                    &gmx_hydorder,
 305                    "hydorder",
 306                    "Compute tetrahedrality parameters around a given atom");
 307     registerModule(manager, &gmx_lie, "lie", "Estimate free energy from linear combinations");
 308     registerModule(manager, &gmx_mdmat, "mdmat", "Calculate residue contact maps");
 309     registerModule(
 310             manager, &gmx_mindist, "mindist", "Calculate the minimum distance between two groups");
 311     registerModule(manager, &gmx_nmeig, "nmeig", "Diagonalize the Hessian for normal mode analysis");
 312     registerModule(manager,
 313                    &gmx_nmens,
 314                    "nmens",
 315                    "Generate an ensemble of structures from the normal modes");
 316     registerModule(manager,
 317                    &gmx_nmr,
 318                    "nmr",
 319                    "Analyze nuclear magnetic resonance properties from an energy file");
 320     registerModule(manager,
 321                    &gmx_nmtraj,
 322                    "nmtraj",
 323                    "Generate a virtual oscillating trajectory from an eigenvector");
 324     registerModule(
 325             manager, &gmx_order, "order", "Compute the order parameter per atom for carbon tails");
 326     registerModule(manager,
 327                    &gmx_pme_error,
 328                    "pme_error",
 329                    "Estimate the error of using PME with a given input file");
 330     registerModule(manager, &gmx_polystat, "polystat", "Calculate static properties of polymers");
 331     registerModule(manager,
 332                    &gmx_potential,
 333                    "potential",
 334                    "Calculate the electrostatic potential across the box");
 335     registerModule(manager,
 336                    &gmx_principal,
 337                    "principal",
 338                    "Calculate principal axes of inertia for a group of atoms");
 339     registerModule(manager, &gmx_rama, "rama", "Compute Ramachandran plots");
 340     registerModule(manager,
 341                    &gmx_rms,
 342                    "rms",
 343                    "Calculate RMSDs with a reference structure and RMSD matrices");
 344     registerModule(manager,
 345                    &gmx_rmsdist,
 346                    "rmsdist",
 347                    "Calculate atom pair distances averaged with power -2, -3 or -6");
 348     registerModule(manager, &gmx_rmsf, "rmsf", "Calculate atomic fluctuations");
 349     registerModule(manager,
 350                    &gmx_rotacf,
 351                    "rotacf",
 352                    "Calculate the rotational correlation function for molecules");
 353     registerModule(manager,
 354                    &gmx_rotmat,
 355                    "rotmat",
 356                    "Plot the rotation matrix for fitting to a reference structure");
 357     registerModule(manager, &gmx_saltbr, "saltbr", "Compute salt bridges");
 358     registerModule(manager, &gmx_sans, "sans", "Compute small angle neutron scattering spectra");
 359     registerModule(manager, &gmx_saxs, "saxs", "Compute small angle X-ray scattering spectra");
 360     registerModule(
 361             manager, &gmx_sham, "sham", "Compute free energies or other histograms from histograms");
 362     registerModule(manager,
 363                    &gmx_sigeps,
 364                    "sigeps",
 365                    "Convert c6/12 or c6/cn combinations to and from sigma/epsilon");
 366     registerModule(manager, &gmx_sorient, "sorient", "Analyze solvent orientation around solutes");
 367     registerModule(manager, &gmx_spatial, "spatial", "Calculate the spatial distribution function");
 368     registerModule(manager,
 369                    &gmx_spol,
 370                    "spol",
 371                    "Analyze solvent dipole orientation and polarization around solutes");
 372     registerModule(manager, &gmx_tcaf, "tcaf", "Calculate viscosities of liquids");
 373     registerModule(manager,
 374                    &gmx_traj,
 375                    "traj",
 376                    "Plot x, v, f, box, temperature and rotational energy from trajectories");
 377     registerModule(manager,
 378                    &gmx_tune_pme,
 379                    "tune_pme",
 380                    "Time mdrun as a function of PME ranks to optimize settings");
 381     registerModule(manager,
 382                    &gmx_vanhove,
 383                    "vanhove",
 384                    "Compute Van Hove displacement and correlation functions");
 385     registerModule(manager, &gmx_velacc, "velacc", "Calculate velocity autocorrelation functions");
 386     registerModule(manager,
 387                    &gmx_wham,
 388                    "wham",
 389                    "Perform weighted histogram analysis after umbrella sampling");
 390     registerModule(manager, &gmx_wheel, "wheel", "Plot helical wheels");
 391     registerModuleNoNice(manager, &gmx_view, "view", "View a trajectory on an X-Windows terminal");
 392
 393     {
 394         gmx::CommandLineModuleGroup group =
 395                 manager->addModuleGroup("Generating topologies and coordinates");
 396         group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
 397         group.addModule("x2top");
 398         group.addModule("solvate");
 399         group.addModule("insert-molecules");
 400         group.addModule("genconf");
 401         group.addModule("genion");
 402         group.addModule("genrestr");
 403         group.addModule("pdb2gmx");
 404     }
 405     {
 406         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Running a simulation");
 407         group.addModule("grompp");
 408         group.addModule("mdrun");
 409         group.addModule("convert-tpr");
 410     }
 411     {
 412         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Viewing trajectories");
 413         group.addModule("nmtraj");
 414         group.addModule("view");
 415     }
 416     {
 417         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Processing energies");
 418         group.addModule("enemat");
 419         group.addModule("energy");
 420         group.addModuleWithDescription("mdrun",
 421                                        "(Re)calculate energies for trajectory frames with -rerun");
 422     }
 423     {
 424         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Converting files");
 425         group.addModule("editconf");
 426         group.addModule("eneconv");
 427         group.addModule("sigeps");
 428         group.addModule("trjcat");
 429         group.addModule("trjconv");
 430         group.addModule("xpm2ps");
 431     }
 432     {
 433         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Tools");
 434         group.addModule("analyze");
 435         group.addModule("awh");
 436         group.addModule("filter");
 437         group.addModule("lie");
 438         group.addModule("pme_error");
 439         group.addModule("sham");
 440         group.addModule("spatial");
 441         group.addModule("traj");
 442         group.addModule("tune_pme");
 443         group.addModule("wham");
 444         group.addModule("check");
 445         group.addModule("dump");
 446         group.addModule("make_ndx");
 447         group.addModule("mk_angndx");
 448         group.addModule("trjorder");
 449         group.addModule("xpm2ps");
 450         group.addModule("report-methods");
 451     }
 452     {
 453         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Distances between structures");
 454         group.addModule("cluster");
 455         group.addModule("confrms");
 456         group.addModule("rms");
 457         group.addModule("rmsf");
 458     }
 459     {
 460         gmx::CommandLineModuleGroup group =
 461                 manager->addModuleGroup("Distances in structures over time");
 462         group.addModule("mindist");
 463         group.addModule("mdmat");
 464         group.addModule("polystat");
 465         group.addModule("rmsdist");
 466     }
 467     {
 468         gmx::CommandLineModuleGroup group =
 469                 manager->addModuleGroup("Mass distribution properties over time");
 470         group.addModule("gyrate");
 471         group.addModule("polystat");
 472         group.addModule("rdf");
 473         group.addModule("rotacf");
 474         group.addModule("rotmat");
 475         group.addModule("sans");
 476         group.addModule("saxs");
 477         group.addModule("traj");
 478         group.addModule("vanhove");
 479     }
 480     {
 481         gmx::CommandLineModuleGroup group =
 482                 manager->addModuleGroup("Analyzing bonded interactions");
 483         group.addModule("angle");
 484         group.addModule("mk_angndx");
 485     }
 486     {
 487         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Structural properties");
 488         group.addModule("bundle");
 489         group.addModule("clustsize");
 490         group.addModule("disre");
 491         group.addModule("hbond");
 492         group.addModule("order");
 493         group.addModule("principal");
 494         group.addModule("rdf");
 495         group.addModule("saltbr");
 496         group.addModule("sorient");
 497         group.addModule("spol");
 498     }
 499     {
 500         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Kinetic properties");
 501         group.addModule("bar");
 502         group.addModule("current");
 503         group.addModule("dos");
 504         group.addModule("dyecoupl");
 505         group.addModule("principal");
 506         group.addModule("tcaf");
 507         group.addModule("traj");
 508         group.addModule("vanhove");
 509         group.addModule("velacc");
 510     }
 511     {
 512         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Electrostatic properties");
 513         group.addModule("current");
 514         group.addModule("dielectric");
 515         group.addModule("dipoles");
 516         group.addModule("potential");
 517         group.addModule("spol");
 518         group.addModule("genion");
 519     }
 520     {
 521         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Protein-specific analysis");
 522         group.addModule("do_dssp");
 523         group.addModule("chi");
 524         group.addModule("helix");
 525         group.addModule("helixorient");
 526         group.addModule("rama");
 527         group.addModule("wheel");
 528     }
 529     {
 530         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Interfaces");
 531         group.addModule("bundle");
 532         group.addModule("density");
 533         group.addModule("densmap");
 534         group.addModule("densorder");
 535         group.addModule("h2order");
 536         group.addModule("hydorder");
 537         group.addModule("order");
 538         group.addModule("potential");
 539     }
 540     {
 541         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Covariance analysis");
 542         group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
 543         group.addModule("covar");
 544         group.addModule("make_edi");
 545     }
 546     {
 547         gmx::CommandLineModuleGroup group = manager->addModuleGroup("Normal modes");
 548         group.addModuleWithDescription("anaeig", "Analyze the normal modes");
 549         group.addModule("nmeig");
 550         group.addModule("nmtraj");
 551         group.addModule("nmens");
 552         group.addModule("grompp");
 553         group.addModuleWithDescription("mdrun",
 554                                        "Find a potential energy minimum and calculate the Hessian");
 555     }
 556 }