diff --git a/modules/mol/mm/doc/buildingblock.rst b/modules/mol/mm/doc/buildingblock.rst
index 2194e6c150de6713bbfbff505ffbb62d8231f91c..83e24d7d988ee2480dcff8e17d220736a82fb432 100644
--- a/modules/mol/mm/doc/buildingblock.rst
+++ b/modules/mol/mm/doc/buildingblock.rst
@@ -14,6 +14,9 @@ Blockmodifiers come in, with the GromacsBlockModifier as a specific
implementation. As a special case there also exist HydrogenConstructors.
+The BuildingBlock Class
+--------------------------------------------------------------------------------
+
.. class:: BuildingBlock
.. method:: Match(residue, [,match_connectivity=True])
@@ -227,7 +230,7 @@ implementation. As a special case there also exist HydrogenConstructors.
.. method:: GetConstraints()
:returns: :class:`list` of all constraints
-Automated modification of :class:`BuildingBlock` and :class:`ResidueHandle`
+Block Modifiers
--------------------------------------------------------------------------------
.. class:: GromacsBlockModifier
@@ -321,6 +324,9 @@ Automated modification of :class:`BuildingBlock` and :class:`ResidueHandle`
:param cmap: :class:`Interaction` cmap to be added
+Hydrogen Constructors
+--------------------------------------------------------------------------------
+
.. class:: GromacsHydrogenConstructor
The :class:`GromacsHydrogenConstructor` is the gromacs way of adding
diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
index 011def6a712c6f0880071cf097d008553e315f29..7765ef0ab98bf12858e3719c25acb3d4e9b80add 100644
--- a/modules/mol/mm/doc/integrators.rst
+++ b/modules/mol/mm/doc/integrators.rst
@@ -7,6 +7,11 @@ The Integrators are a wrapper around the integrators provided by OpenMM and
have to be attached to the :class:`Settings` when setting up a simulation
to provide a way of making the thing shake.
+
+
+Verlet Dynamics
+--------------------------------------------------------------------------------
+
.. class:: VerletIntegrator(step_size)
Implementation of Verlet dynamics
@@ -15,9 +20,27 @@ to provide a way of making the thing shake.
-.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
+.. class:: VariableVerletIntegrator(error_tol)
- Implementation of Brownian dynamics
+ Implementation of Verlet dynamics with variable time steps
+
+ :param error_tol: :class:`float` error tolerance
+
+ .. method:: GetErrorTolerance()
+
+ :returns: :class:`float`
+
+ .. method:: SetErrorTolerance(tol)
+
+ :param tol: :class:`float`
+
+
+Langevin Dynamics
+--------------------------------------------------------------------------------
+
+.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
+
+ Implementation of the Langevin dynamics
:param temperature: :class:`float` temperature of heat bath in K
@@ -28,7 +51,7 @@ to provide a way of making the thing shake.
.. method:: GetTemperature()
- :returns: :class:`float`
+ :returns: :class:`float`
.. method:: SetTemperature(temperature)
@@ -53,16 +76,16 @@ to provide a way of making the thing shake.
-.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
+.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
- Implementation of the Langevin dynamics
+ Implementation of Langevin dynamics with variable time steps
:param temperature: :class:`float` temperature of heat bath in K
:param friction_coeff: :class:`float` friction coefficient coupling the
system to the heat bath in 1/ps
- :param step_size: :class:`float` defining timestep in ps.
+ :param error_tol: :class:`float` error_tolerance.
.. method:: GetTemperature()
@@ -88,38 +111,32 @@ to provide a way of making the thing shake.
:param seed: :class:`int`
-
-
-.. class:: VariableVerletIntegrator(error_tol)
-
- Implementation of Verlet dynamics with variable time steps
-
- :param error_tol: :class:`float` error tolerance
-
.. method:: GetErrorTolerance()
:returns: :class:`float`
- .. method:: SetErrorTolerance(tol)
+ .. method:: SetErrorTolerance()
:param tol: :class:`float`
+Brownian Dynamics
+--------------------------------------------------------------------------------
-.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
+.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
- Implementation of Langevin dynamics with variable time steps
+ Implementation of Brownian dynamics
:param temperature: :class:`float` temperature of heat bath in K
:param friction_coeff: :class:`float` friction coefficient coupling the
system to the heat bath in 1/ps
- :param error_tol: :class:`float` error_tolerance.
+ :param step_size: :class:`float` defining timestep in ps.
.. method:: GetTemperature()
- :returns: :class:`float`
+ :returns: :class:`float`
.. method:: SetTemperature(temperature)
@@ -140,11 +157,3 @@ to provide a way of making the thing shake.
.. method:: SetRandomNumberSeed(seed)
:param seed: :class:`int`
-
- .. method:: GetErrorTolerance()
-
- :returns: :class:`float`
-
- .. method:: SetErrorTolerance()
-
- :param tol: :class:`float`
diff --git a/modules/mol/mm/doc/interaction.rst b/modules/mol/mm/doc/interaction.rst
index a1eff84d13f62de3c4c3d147da6c3dec5a5fca21..110d662c6f70ec9f9de7c947b8163e88284bf949 100644
--- a/modules/mol/mm/doc/interaction.rst
+++ b/modules/mol/mm/doc/interaction.rst
@@ -108,6 +108,9 @@ Interaction Parametrization
+The Interaction Class
+--------------------------------------------------------------------------------
+
.. class:: Interaction(func_type)
:param func_type: :class:`FuncType` defining a particular interaction
diff --git a/modules/mol/mm/doc/observers.rst b/modules/mol/mm/doc/observers.rst
index b0a7fade2f11862657a0e4bb314662d8f8e755f6..d681cff5faf92e907125392410289ad04ff11d08 100644
--- a/modules/mol/mm/doc/observers.rst
+++ b/modules/mol/mm/doc/observers.rst
@@ -7,6 +7,9 @@ Observers can be registered to a :class:`Simulation` and get called at a
defined interval.
+Trajectory Observers
+--------------------------------------------------------------------------------
+
.. class:: TrajObserver(rythm)
Stores and updates the MD trajectory produced by a :class:`Simulation`
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index 9073856de3451cd655cb650e471eefab62cb986c..b7ee94e6532b04027885d39ef650b9053264d71b 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -47,13 +47,22 @@ mapped back to the attached structure at any time.
in **topology**
- .. method:: Save(filename)
+ .. method:: Save(filename, settings)
+
+ Dumps current status of the simulation with its connected **entity** onto
+ disk. All informations from the **entity** except plain chains, residues,
+ atoms and bonds are lost.
:param filename: :class:`str`
.. method:: Load(filename)
+ Loads dumped simulation from disk. You have to make sure, that the provided
+ settings are consistent with those from the saved simualtion. Undefined
+ behaviour must be expected otherwise.
+
:param filename: :class:`str`
+ :param settings: :class:`ost.mm.Settings`
.. method:: ApplyLBFGS([tolerance=1.0,max_iterations=1000])