diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a9cfe9654f..a6f3d75817 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -106,6 +106,9 @@ it gives quick access to documentation for all LAMMPS commands.
 .. toctree::
    :maxdepth: 2
    :numbered:
+   :caption: User Documentation
+   :name: userdoc
+   :includehidden:
    
    Section_intro
    Section_start
@@ -121,6 +124,20 @@ it gives quick access to documentation for all LAMMPS commands.
    Section_errors
    Section_history
 
+.. toctree::
+   :caption: Index
+   :name: index
+   :hidden:
+
+   tutorials
+   commands
+   fixes
+   computes
+   pairs
+   bonds
+   angles
+   dihedrals
+   impropers
 
 Indices and tables
 ==================
diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt
index ed6a233a2d..fcdcb2d41c 100644
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@@ -157,11 +157,25 @@ packages"_Section_packages.html.
 These are the accelerator packages
 currently in LAMMPS, either as standard or user packages:
 
-"GPU Package"_accelerate_gpu.html with CUDA and OpenCL support for Nvidia GPUs and others :h5
-"USER-INTEL Package"_accelerate_intel.html for Intel CPUs and Intel Xeon Phi :h5
-"KOKKOS Package"_accelerate_kokkos.html for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading :h5
-"USER-OMP Package "_accelerate_omp.html for OpenMP threading and generic CPU optimizations :h5
-"OPT Package"_accelerate_opt.html generic CPU optimizations :h5
+"GPU Package"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
+"USER-INTEL Package"_accelerate_intel.html : for Intel CPUs and Intel Xeon Phi
+"KOKKOS Package"_accelerate_kokkos.html : for Nvidia GPUs, Intel Xeon Phi, and OpenMP threading
+"USER-OMP Package"_accelerate_omp.html : for OpenMP threading and generic CPU optimizations
+"OPT Package"_accelerate_opt.html : generic CPU optimizations :tb(s=:)
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+
+   accelerate_gpu
+   accelerate_intel
+   accelerate_kokkos
+   accelerate_omp
+   accelerate_opt
+
+END_RST -->
 
 Inverting this list, LAMMPS currently has acceleration support for
 three kinds of hardware, via the listed packages:
diff --git a/doc/src/angles.txt b/doc/src/angles.txt
new file mode 100644
index 0000000000..ff1f68d45a
--- /dev/null
+++ b/doc/src/angles.txt
@@ -0,0 +1,27 @@
+Angle Styles :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   angle_charmm
+   angle_class2
+   angle_cosine
+   angle_cosine_delta
+   angle_cosine_periodic
+   angle_cosine_shift
+   angle_cosine_shift_exp
+   angle_cosine_squared
+   angle_dipole
+   angle_fourier
+   angle_fourier_simple
+   angle_harmonic
+   angle_hybrid
+   angle_none
+   angle_quartic
+   angle_sdk
+   angle_table
+   angle_zero
+
+END_RST -->
diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt
new file mode 100644
index 0000000000..fdc3d23c13
--- /dev/null
+++ b/doc/src/bonds.txt
@@ -0,0 +1,22 @@
+Bonds :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   bond_class2
+   bond_fene
+   bond_fene_expand
+   bond_harmonic
+   bond_harmonic_shift
+   bond_harmonic_shift_cut
+   bond_hybrid
+   bond_morse
+   bond_none
+   bond_nonlinear
+   bond_quartic
+   bond_table
+   bond_zero
+
+END_RST -->
diff --git a/doc/src/commands.txt b/doc/src/commands.txt
new file mode 100644
index 0000000000..958a6f34f4
--- /dev/null
+++ b/doc/src/commands.txt
@@ -0,0 +1,109 @@
+Commands :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   angle_coeff
+   angle_style
+   atom_modify
+   atom_style
+   balance
+   bond_coeff
+   bond_style
+   bond_write
+   boundary
+   box
+   change_box
+   clear
+   comm_modify
+   comm_style
+   compute
+   compute_modify
+   create_atoms
+   create_bonds
+   create_box
+   delete_atoms
+   delete_bonds
+   dielectric
+   dihedral_coeff
+   dihedral_style
+   dimension
+   displace_atoms
+   dump
+   dump_custom_vtk
+   dump_h5md
+   dump_image
+   dump_modify
+   dump_molfile
+   echo
+   fix
+   fix_modify
+   group
+   group2ndx
+   if
+   improper_coeff
+   improper_style
+   include
+   info
+   jump
+   kspace_modify
+   kspace_style
+   label
+   lattice
+   log
+   mass
+   min_modify
+   min_style
+   minimize
+   molecule
+   neb
+   neigh_modify
+   neighbor
+   newton
+   next
+   package
+   pair_coeff
+   pair_modify
+   pair_style
+   pair_write
+   partition
+   prd
+   print
+   processors
+   python
+   quit
+   read_data
+   read_dump
+   read_restart
+   region
+   replicate
+   rerun
+   reset_timestep
+   restart
+   run
+   run_style
+   set
+   shell
+   special_bonds
+   suffix
+   tad
+   temper
+   thermo
+   thermo_modify
+   thermo_style
+   timer
+   timestep
+   uncompute
+   undump
+   unfix
+   units
+   variable
+   velocity
+   write_coeff
+   write_data
+   write_dump
+   write_restart
+
+END_RST -->
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
new file mode 100644
index 0000000000..e7e54a6b3b
--- /dev/null
+++ b/doc/src/computes.txt
@@ -0,0 +1,120 @@
+Computes :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   compute_ackland_atom
+   compute_angle
+   compute_angle_local
+   compute_angmom_chunk
+   compute_basal_atom
+   compute_body_local
+   compute_bond
+   compute_bond_local
+   compute_centro_atom
+   compute_chunk_atom
+   compute_cluster_atom
+   compute_cna_atom
+   compute_com
+   compute_com_chunk
+   compute_contact_atom
+   compute_coord_atom
+   compute_damage_atom
+   compute_dihedral
+   compute_dihedral_local
+   compute_dilatation_atom
+   compute_dipole_chunk
+   compute_displace_atom
+   compute_dpd
+   compute_dpd_atom
+   compute_erotate_asphere
+   compute_erotate_rigid
+   compute_erotate_sphere
+   compute_erotate_sphere_atom
+   compute_event_displace
+   compute_fep
+   compute_group_group
+   compute_gyration
+   compute_gyration_chunk
+   compute_heat_flux
+   compute_hexorder_atom
+   compute_improper
+   compute_improper_local
+   compute_inertia_chunk
+   compute_ke
+   compute_ke_atom
+   compute_ke_atom_eff
+   compute_ke_eff
+   compute_ke_rigid
+   compute_meso_e_atom
+   compute_meso_rho_atom
+   compute_meso_t_atom
+   compute_msd
+   compute_msd_chunk
+   compute_msd_nongauss
+   compute_omega_chunk
+   compute_orientorder_atom
+   compute_pair
+   compute_pair_local
+   compute_pe
+   compute_pe_atom
+   compute_plasticity_atom
+   compute_pressure
+   compute_property_atom
+   compute_property_chunk
+   compute_property_local
+   compute_rdf
+   compute_reduce
+   compute_rigid_local
+   compute_saed
+   compute_slice
+   compute_smd_contact_radius
+   compute_smd_damage
+   compute_smd_hourglass_error
+   compute_smd_internal_energy
+   compute_smd_plastic_strain
+   compute_smd_plastic_strain_rate
+   compute_smd_rho
+   compute_smd_tlsph_defgrad
+   compute_smd_tlsph_dt
+   compute_smd_tlsph_num_neighs
+   compute_smd_tlsph_shape
+   compute_smd_tlsph_strain
+   compute_smd_tlsph_strain_rate
+   compute_smd_tlsph_stress
+   compute_smd_triangle_mesh_vertices
+   compute_smd_ulsph_num_neighs
+   compute_smd_ulsph_strain
+   compute_smd_ulsph_strain_rate
+   compute_smd_ulsph_stress
+   compute_smd_vol
+   compute_sna_atom
+   compute_stress_atom
+   compute_tally
+   compute_temp
+   compute_temp_asphere
+   compute_temp_body
+   compute_temp_chunk
+   compute_temp_com
+   compute_temp_cs
+   compute_temp_deform
+   compute_temp_deform_eff
+   compute_temp_drude
+   compute_temp_eff
+   compute_temp_partial
+   compute_temp_profile
+   compute_temp_ramp
+   compute_temp_region
+   compute_temp_region_eff
+   compute_temp_rotate
+   compute_temp_sphere
+   compute_ti
+   compute_torque_chunk
+   compute_vacf
+   compute_vcm_chunk
+   compute_voronoi_atom
+   compute_xrd
+
+END_RST -->
diff --git a/doc/src/dihedrals.txt b/doc/src/dihedrals.txt
new file mode 100644
index 0000000000..500a6a52bf
--- /dev/null
+++ b/doc/src/dihedrals.txt
@@ -0,0 +1,39 @@
+Dihedral Styles :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   dihedral_charmm
+   dihedral_class2
+   dihedral_cosine_shift_exp
+   dihedral_fourier
+   dihedral_harmonic
+   dihedral_helix
+   dihedral_hybrid
+   dihedral_multi_harmonic
+   dihedral_nharmonic
+   dihedral_none
+   dihedral_opls
+   dihedral_quadratic
+   dihedral_spherical
+   dihedral_table
+   dihedral_zero
+   dihedral_charmm
+   dihedral_class2
+   dihedral_cosine_shift_exp
+   dihedral_fourier
+   dihedral_harmonic
+   dihedral_helix
+   dihedral_hybrid
+   dihedral_multi_harmonic
+   dihedral_nharmonic
+   dihedral_none
+   dihedral_opls
+   dihedral_quadratic
+   dihedral_spherical
+   dihedral_table
+   dihedral_zero
+
+END_RST -->
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
new file mode 100644
index 0000000000..48a4c805a4
--- /dev/null
+++ b/doc/src/fixes.txt
@@ -0,0 +1,157 @@
+Fixes :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   fix_adapt
+   fix_adapt_fep
+   fix_addforce
+   fix_addtorque
+   fix_append_atoms
+   fix_atc
+   fix_atom_swap
+   fix_ave_atom
+   fix_ave_chunk
+   fix_ave_correlate
+   fix_ave_correlate_long
+   fix_ave_histo
+   fix_ave_time
+   fix_aveforce
+   fix_balance
+   fix_bond_break
+   fix_bond_create
+   fix_bond_swap
+   fix_box_relax
+   fix_colvars
+   fix_controller
+   fix_deform
+   fix_deposit
+   fix_drag
+   fix_drude
+   fix_drude_transform
+   fix_dt_reset
+   fix_efield
+   fix_ehex
+   fix_enforce2d
+   fix_eos_cv
+   fix_eos_table
+   fix_eos_table_rx
+   fix_evaporate
+   fix_external
+   fix_flow_gauss
+   fix_freeze
+   fix_gcmc
+   fix_gld
+   fix_gle
+   fix_gravity
+   fix_heat
+   fix_imd
+   fix_indent
+   fix_ipi
+   fix_langevin
+   fix_langevin_drude
+   fix_langevin_eff
+   fix_lb_fluid
+   fix_lb_momentum
+   fix_lb_pc
+   fix_lb_rigid_pc_sphere
+   fix_lb_viscous
+   fix_lineforce
+   fix_manifoldforce
+   fix_meso
+   fix_meso_stationary
+   fix_momentum
+   fix_move
+   fix_msst
+   fix_neb
+   fix_nh
+   fix_nh_eff
+   fix_nph_asphere
+   fix_nph_body
+   fix_nph_sphere
+   fix_nphug
+   fix_npt_asphere
+   fix_npt_body
+   fix_npt_sphere
+   fix_nve
+   fix_nve_asphere
+   fix_nve_asphere_noforce
+   fix_nve_body
+   fix_nve_eff
+   fix_nve_limit
+   fix_nve_line
+   fix_nve_manifold_rattle
+   fix_nve_noforce
+   fix_nve_sphere
+   fix_nve_tri
+   fix_nvt_asphere
+   fix_nvt_body
+   fix_nvt_manifold_rattle
+   fix_nvt_sllod
+   fix_nvt_sllod_eff
+   fix_nvt_sphere
+   fix_oneway
+   fix_orient
+   fix_phonon
+   fix_pimd
+   fix_planeforce
+   fix_poems
+   fix_pour
+   fix_press_berendsen
+   fix_print
+   fix_property_atom
+   fix_qbmsst
+   fix_qeq
+   fix_qeq_comb
+   fix_qeq_reax
+   fix_qmmm
+   fix_qtb
+   fix_reax_bonds
+   fix_reaxc_species
+   fix_recenter
+   fix_restrain
+   fix_rigid
+   fix_rx
+   fix_saed_vtk
+   fix_setforce
+   fix_shake
+   fix_shardlow
+   fix_smd
+   fix_smd_adjust_dt
+   fix_smd_integrate_tlsph
+   fix_smd_integrate_ulsph
+   fix_smd_move_triangulated_surface
+   fix_smd_setvel
+   fix_smd_tlsph_reference_configuration
+   fix_smd_wall_surface
+   fix_spring
+   fix_spring_chunk
+   fix_spring_rg
+   fix_spring_self
+   fix_srd
+   fix_store_force
+   fix_store_state
+   fix_temp_berendsen
+   fix_temp_csvr
+   fix_temp_rescale
+   fix_temp_rescale_eff
+   fix_tfmc
+   fix_thermal_conductivity
+   fix_ti_rs
+   fix_ti_spring
+   fix_tmd
+   fix_ttm
+   fix_tune_kspace
+   fix_vector
+   fix_viscosity
+   fix_viscous
+   fix_wall
+   fix_wall_gran
+   fix_wall_piston
+   fix_wall_reflect
+   fix_wall_region
+   fix_wall_srd
+
+END_RST -->
diff --git a/doc/src/impropers.txt b/doc/src/impropers.txt
new file mode 100644
index 0000000000..ced6128879
--- /dev/null
+++ b/doc/src/impropers.txt
@@ -0,0 +1,20 @@
+Improper Styles :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   improper_class2
+   improper_cossq
+   improper_cvff
+   improper_distance
+   improper_fourier
+   improper_harmonic
+   improper_hybrid
+   improper_none
+   improper_ring
+   improper_umbrella
+   improper_zero
+
+END_RST -->
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
new file mode 100644
index 0000000000..77f4fba807
--- /dev/null
+++ b/doc/src/pairs.txt
@@ -0,0 +1,102 @@
+Pair Styles :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   pair_adp
+   pair_airebo
+   pair_awpmd
+   pair_beck
+   pair_body
+   pair_bop
+   pair_born
+   pair_brownian
+   pair_buck
+   pair_buck_long
+   pair_charmm
+   pair_class2
+   pair_colloid
+   pair_comb
+   pair_coul
+   pair_coul_diel
+   pair_cs
+   pair_dipole
+   pair_dpd
+   pair_dpd_fdt
+   pair_dsmc
+   pair_eam
+   pair_edip
+   pair_eff
+   pair_eim
+   pair_exp6_rx
+   pair_gauss
+   pair_gayberne
+   pair_gran
+   pair_gromacs
+   pair_hbond_dreiding
+   pair_hybrid
+   pair_kim
+   pair_lcbop
+   pair_line_lj
+   pair_list
+   pair_lj
+   pair_lj96
+   pair_lj_cubic
+   pair_lj_expand
+   pair_lj_long
+   pair_lj_sf
+   pair_lj_smooth
+   pair_lj_smooth_linear
+   pair_lj_soft
+   pair_lubricate
+   pair_lubricateU
+   pair_mdf
+   pair_meam
+   pair_meam_spline
+   pair_meam_sw_spline
+   pair_mgpt
+   pair_mie
+   pair_morse
+   pair_multi_lucy
+   pair_multi_lucy_rx
+   pair_nb3b_harmonic
+   pair_nm
+   pair_none
+   pair_peri
+   pair_polymorphic
+   pair_quip
+   pair_reax
+   pair_reax_c
+   pair_resquared
+   pair_sdk
+   pair_smd_hertz
+   pair_smd_tlsph
+   pair_smd_triangulated_surface
+   pair_smd_ulsph
+   pair_smtbq
+   pair_snap
+   pair_soft
+   pair_sph_heatconduction
+   pair_sph_idealgas
+   pair_sph_lj
+   pair_sph_rhosum
+   pair_sph_taitwater
+   pair_sph_taitwater_morris
+   pair_srp
+   pair_sw
+   pair_table
+   pair_table_rx
+   pair_tersoff
+   pair_tersoff_mod
+   pair_tersoff_zbl
+   pair_thole
+   pair_tri_lj
+   pair_vashishta
+   pair_yukawa
+   pair_yukawa_colloid
+   pair_zbl
+   pair_zero
+
+END_RST -->
diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt
new file mode 100644
index 0000000000..98c748f3af
--- /dev/null
+++ b/doc/src/tutorials.txt
@@ -0,0 +1,13 @@
+Tutorials :h1
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   tutorial_drude
+   tutorial_github
+   body
+   manifolds
+
+END_RST -->