registerModule(manager, &gmx_covar, "covar",
"Calculate and diagonalize the covariance matrix");
registerModule(manager, &gmx_current, "current",
- "Calculate dielectric constants and charge autocorrelation function");
+ "Calculate dielectric constants and current autocorrelation function");
registerModule(manager, &gmx_density, "density",
"Calculate the density of the system");
registerModule(manager, &gmx_densmap, "densmap",
registerModule(manager, &gmx_saltbr, "saltbr",
"Compute salt bridges");
registerModule(manager, &gmx_sans, "sans",
- "Compute the small angle neutron scattering spectra");
+ "Compute small angle neutron scattering spectra");
registerModule(manager, &gmx_sas, "sas",
"Compute solvent accessible surface area");
registerModule(manager, &gmx_saxs, "saxs",
- "Calculates SAXS structure factors based on Cromer's method");
+ "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_tune_pme, "tune_pme",
"Time mdrun as a function of PME nodes to optimize settings");
registerModule(manager, &gmx_vanhove, "vanhove",
- "Compute Van Hove correlation functions");
+ "Compute Van Hove displacement and correlation functions");
registerModule(manager, &gmx_velacc, "velacc",
"Calculate velocity autocorrelation functions");
registerModule(manager, &gmx_wham, "wham",
registerModule(manager, &gmx_view, "view",
"View a trajectory on an X-Windows terminal");
- // TODO: Also include binaries from other directories than src/tools/:
- // "mdrun|finds a potential energy minimum and calculates the Hessian");
- // "mdrun|with -rerun (re)calculates energies for trajectory frames");
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Generating topologies and coordinates");
+ group.addModuleWithDescription("editconf", "Edit the box and write subgroups");
+ group.addModule("protonate");
+ group.addModule("x2top");
+ group.addModule("genbox");
+ group.addModule("genconf");
+ group.addModule("genion");
+ group.addModule("genrestr");
+ group.addModule("pdb2gmx");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Running a simulation");
+ group.addModule("grompp");
+ group.addModule("mdrun");
+ group.addModule("tpbconv");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Viewing trajectories");
+ group.addModule("nmtraj");
+ group.addModule("view");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Processing energies");
+ group.addModule("enemat");
+ group.addModule("energy");
+ group.addModuleWithDescription("mdrun", "(Re)calculate energies for trajectory frames with -rerun");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Converting files");
+ group.addModule("editconf");
+ group.addModule("eneconv");
+ group.addModule("sigeps");
+ group.addModule("trjcat");
+ group.addModule("trjconv");
+ group.addModule("xpm2ps");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Tools");
+ group.addModule("analyze");
+ group.addModule("dyndom");
+ group.addModule("filter");
+ group.addModule("lie");
+ group.addModule("morph");
+ group.addModule("pme_error");
+ group.addModule("sham");
+ group.addModule("spatial");
+ group.addModule("traj");
+ group.addModule("tune_pme");
+ group.addModule("wham");
+ group.addModule("check");
+ group.addModule("dump");
+ group.addModule("make_ndx");
+ group.addModule("mk_angndx");
+ group.addModule("trjorder");
+ group.addModule("xpm2ps");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Distances between structures");
+ group.addModule("cluster");
+ group.addModule("confrms");
+ group.addModule("rms");
+ group.addModule("rmsf");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Distances in structures over time");
+ group.addModule("mindist");
+ group.addModule("mdmat");
+ group.addModule("polystat");
+ group.addModule("rmsdist");
+ }
+ {
+ 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");
+ group.addModule("rotmat");
+ group.addModule("sans");
+ group.addModule("saxs");
+ group.addModule("traj");
+ group.addModule("vanhove");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Analyzing bonded interactions");
+ group.addModule("angle");
+ group.addModule("mk_angndx");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Structural properties");
+ group.addModule("anadock");
+ group.addModule("bundle");
+ group.addModule("clustsize");
+ group.addModule("disre");
+ group.addModule("hbond");
+ group.addModule("order");
+ group.addModule("principal");
+ group.addModule("rdf");
+ group.addModule("saltbr");
+ group.addModule("sas");
+ group.addModule("sorient");
+ group.addModule("spol");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Kinetic properties");
+ group.addModule("bar");
+ group.addModule("current");
+ group.addModule("dos");
+ group.addModule("dyecoupl");
+ group.addModule("kinetics");
+ group.addModule("principal");
+ group.addModule("tcaf");
+ group.addModule("traj");
+ group.addModule("vanhove");
+ group.addModule("velacc");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Electrostatic properties");
+ group.addModule("current");
+ group.addModule("dielectric");
+ group.addModule("dipoles");
+ group.addModule("potential");
+ group.addModule("spol");
+ group.addModule("genion");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Protein-specific analysis");
+ group.addModule("do_dssp");
+ group.addModule("chi");
+ group.addModule("helix");
+ group.addModule("helixorient");
+ group.addModule("rama");
+ group.addModule("wheel");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Interfaces");
+ group.addModule("bundle");
+ group.addModule("density");
+ group.addModule("densmap");
+ group.addModule("densorder");
+ group.addModule("h2order");
+ group.addModule("hydorder");
+ group.addModule("order");
+ group.addModule("potential");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Covariance analysis");
+ group.addModuleWithDescription("anaeig", "Analyze the eigenvectors");
+ group.addModule("covar");
+ group.addModule("make_edi");
+ }
+ {
+ gmx::CommandLineModuleGroup group =
+ manager->addModuleGroup("Normal modes");
+ group.addModuleWithDescription("anaeig", "Analyze the normal modes");
+ group.addModule("nmeig");
+ group.addModule("nmtraj");
+ group.addModule("nmens");
+ group.addModule("grompp");
+ group.addModuleWithDescription("mdrun", "Find a potential energy minimum and calculate the Hessian");
+ }
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff