First import

Doc/Examples/DNA/construction.py.rst

+:orphan:
+
+Constructing a DNA strand with a ligand
+#######################################
+
+.. literalinclude:: ../../../Examples/DNA/construction.py
+   :language: python
+   :linenos:
+

Doc/Examples/Forcefield/ElectricField/Cython/ElectricField.py.rst

+:orphan:
+
+An electric field term (Python part)
+####################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/ElectricField/Cython/ElectricField.py
+   :language: python
+   :linenos:
+

Doc/Examples/Forcefield/ElectricField/Cython/MMTK_electric_field.pyx.rst

+:orphan:
+
+An electric field term (Cython part)
+####################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/ElectricField/Cython/MMTK_electric_field.pyx
+   :language: cython
+   :linenos:
+

Doc/Examples/Forcefield/ElectricField/Python/ElectricField.py.rst

+:orphan:
+
+An electric field term implemented in pure Python
+#################################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/ElectricField/Python/ElectricField.py
+   :language: python
+   :linenos:
+

Doc/Examples/Forcefield/HarmonicOscillator/Cython/HarmonicOscillatorFF.py.rst

+:orphan:
+
+An efficient harmonic oscillator term (Python part)
+###################################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/HarmonicOscillator/Cython/HarmonicOscillatorFF.py
+   :language: python
+   :linenos:
+

Doc/Examples/Forcefield/HarmonicOscillator/Cython/MMTK_harmonic_oscillator.pyx.rst

+:orphan:
+
+An efficient harmonic oscillator term (Cython part)
+###################################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/HarmonicOscillator/Cython/MMTK_harmonic_oscillator.pyx
+   :language: cython
+   :linenos:
+

Doc/Examples/Forcefield/HarmonicOscillator/Python/HarmonicOscillatorFF.py.rst

+:orphan:
+
+A harmonic oscillator term in pure Python
+#########################################
+
+.. literalinclude:: ../../../../../Examples/Forcefield/HarmonicOscillator/Python/HarmonicOscillatorFF.py
+   :language: python
+   :linenos:
+

Doc/Examples/LangevinDynamics/LangevinDynamics.py.rst

+:orphan:
+
+An integrator for Langevin dynamics (Python part)
+#################################################
+
+.. literalinclude:: ../../../Examples/LangevinDynamics/LangevinDynamics.py
+   :language: python
+   :linenos:
+

Doc/Examples/LangevinDynamics/MMTK_langevin.c.rst

+:orphan:
+
+An integrator for Langevin dynamics (C part)
+############################################
+
+.. literalinclude:: ../../../Examples/LangevinDynamics/MMTK_langevin.c
+   :language: c
+   :linenos:
+

Doc/Examples/MDIntegrator/VelocityVerlet.pyx.rst

+:orphan:
+
+A simple Velocity Verlet integrator
+###################################
+
+.. literalinclude:: ../../../Examples/MDIntegrator/VelocityVerlet.pyx
+   :language: cython
+   :linenos:
+

Doc/Examples/MPI/md.py.rst

+:orphan:
+
+Protein solvation in parallel
+#############################
+
+.. literalinclude:: ../../../Examples/MPI/md.py
+   :language: python
+   :linenos:
+

Doc/Examples/Miscellaneous/charge_fit.py.rst

+:orphan:
+
+Fitting point charges to an electrostatic potential surface
+###########################################################
+
+.. literalinclude:: ../../../Examples/Miscellaneous/charge_fit.py
+   :language: python
+   :linenos:
+

Doc/Examples/Miscellaneous/construct_from_pdb.py.rst

+:orphan:
+
+Building a complete universe from a PDB file
+############################################
+
+.. literalinclude:: ../../../Examples/Miscellaneous/construct_from_pdb.py
+   :language: python
+   :linenos:
+

Doc/Examples/Miscellaneous/lattice.py.rst

+:orphan:
+
+Place molecules on a lattice
+############################
+
+.. literalinclude:: ../../../Examples/Miscellaneous/lattice.py
+   :language: python
+   :linenos:
+

Doc/Examples/Miscellaneous/vector_field.py.rst

+:orphan:
+
+Vector fields for analysis and visualization of collective motions
+##################################################################
+
+.. literalinclude:: ../../../Examples/Miscellaneous/vector_field.py
+   :language: python
+   :linenos:
+

Doc/Examples/MolecularDynamics/argon.py.rst

+:orphan:
+
+Simulation of liquid argon
+##########################
+
+.. literalinclude:: ../../../Examples/MolecularDynamics/argon.py
+   :language: python
+   :linenos:

Doc/Examples/MolecularDynamics/protein.py.rst

+:orphan:
+
+Simulation of a protein
+#######################
+
+.. literalinclude:: ../../../Examples/MolecularDynamics/protein.py
+   :language: python
+   :linenos:

Doc/Examples/MolecularDynamics/restart.py.rst

+:orphan:
+
+Restarting the protein simulation
+#################################
+
+.. literalinclude:: ../../../Examples/MolecularDynamics/restart.py
+   :language: python
+   :linenos:

Doc/Examples/MolecularDynamics/solvation.py.rst

+:orphan:
+
+Solvation of a protein in water
+###############################
+
+.. literalinclude:: ../../../Examples/MolecularDynamics/solvation.py
+   :language: python
+   :linenos: