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<li><a href="$rootdir$/parallel_c++/README.html">Parallel Programming with C++</a>
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<li><a href="$rootdir$/parallel_c++/part1.html">Part 1: Functional Programming</a>
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<li><a href="$rootdir$/parallel_c++/functions.html">Functions as Objects</a></li>
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<li><a href="$rootdir$/parallel_c++/part2.html">Part 2: Parallel Programming Using Intel Threading Building Blocks</a>
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<li><a href="$rootdir$/parallel_c++/parallel_for.html">tbb::parallel_for</a></li>
<li><a href="$rootdir$/parallel_c++/parallel_reduce.html">tbb::parallel_reduce</a></li>
<li><a href="$rootdir$/parallel_c++/parallel_mapreduce.html">Writing a parallel map/reduce</a></li>
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<li><a href="$rootdir$/vector_c++/README.html">Efficient Vectorisation with C++</a>
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<li><a href="$rootdir$/vector_c++/part1.html">Part 1: Introduction to Vectorisation</a>
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<li><a href="$rootdir$/vector_c++/vectorisation.html">What is Vectorisation?</a></li>
<li><a href="$rootdir$/vector_c++/simd.html">How to Vectorise (omp simd)</a></li>
<li><a href="$rootdir$/vector_c++/features.html">omp simd features</a></li>
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<li><a href="$rootdir$/vector_c++/part2.html">Part 2: Vectorisation using Intrinsics</a>
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<li><a href="$rootdir$/beginning_openmp/README.html">Parallel Programming with OpenMP</a>
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<li><a href="$rootdir$/beginning_mpi/README.html">Parallel Programming with MPI</a>
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<li><a href="$rootdir$/beginning_mpi/reduction.html">Reduction</a></li>
<li><a href="$rootdir$/beginning_mpi/mapreduce.html">Map / Reduce</a></li>
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<li><a href="$rootdir$/inception_workshop/README.html">JupyterHub and Kubernetes</a>
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<li><a href="$rootdir$/inception_workshop/course/part01.html">Creating the workshop</a></li>
<li><a href="$rootdir$/inception_workshop/course/part02.html">Finding all your dependencies</a></li>
<li><a href="$rootdir$/inception_workshop/course/part03.html">Building the docker image</a></li>
<li><a href="$rootdir$/inception_workshop/course/part04.html">JupyterHub</a></li>
<li><a href="$rootdir$/inception_workshop/course/part05.html">Uploading to the cloud</a></li>
<li><a href="$rootdir$/inception_workshop/course/part06.html">Kubernetes</a></li>
<li><a href="$rootdir$/inception_workshop/course/part07.html">Helm</a></li>
<li><a href="$rootdir$/inception_workshop/course/part08.html">Configuring JupyterHub</a></li>
<li><a href="$rootdir$/inception_workshop/course/whatnext.html">What next?</a></li>
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<li><p></p></li>
<li><a href="$rootdir$/intro_to_mc/README.html">Introduction to Monte Carlo</a>
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<li><a href="$rootdir$/intro_to_mc/part1/README.html">Part 1
<ul>
<li><a href="$rootdir$/intro_to_mc/part1/intro.html">Introduction to Monte Carlo</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/software.html">Software</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/metropolis.html">Metropolis Monte Carlo</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/running.html">Running metropolis.py</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/control.html">Control Variables</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/phase.html">Phase Changes</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/ensemble.html">Phase Space and Ensembles</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/volume.html">Volume Moves</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/npt.html">NPT Simulations</a></li>
<li><a href="$rootdir$/intro_to_mc/part1/summary.html">Summary</a></li>
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<li><a href="$rootdir$/intro_to_mc/part2/README.html">Part 2
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<li><a href="$rootdir$/intro_to_mc/part2/intro.html">Introduction and Software</a></li>
<li><a href="$rootdir$/intro_to_mc/part2/rigid.html">Sampling the Solvent - Rigid Body Moves</a></li>
<li><a href="$rootdir$/intro_to_mc/part2/intra.html">Sampling the Ligand - Intramolecular Moves</a></li>
<li><a href="$rootdir$/intro_to_mc/part2/backbone.html">Sampling the Protein - Backbone Moves</a></li>
<li><a href="$rootdir$/intro_to_mc/part2/weight.html">Sampling it all - Weighting Moves</a></li>
<li><a href="$rootdir$/intro_to_mc/part2/whatnext.html">Summary</a></li>
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<li><a href="$rootdir$/dynamics/README.html">Molecular Visualisation, Modelling and Dynamics</a>
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<li><a href="$rootdir$/dynamics/visualisation/README.html">Part 1: Molecular Visualisation</a>
<ul>
<li><a href="$rootdir$/dynamics/visualisation/opening_files.html">1a: Opening Files</a></li>
<li><a href="$rootdir$/dynamics/visualisation/mouse.html">1b: Manipulating the View</a></li>
<li><a href="$rootdir$/dynamics/visualisation/representations.html">1c: Graphical Representations</a></li>
<li><a href="$rootdir$/dynamics/visualisation/selection.html">1d: Selecting Atoms</a></li>
<li><a href="$rootdir$/dynamics/visualisation/complex_selection.html">1e: Complex Selections</a></li>
<li><a href="$rootdir$/dynamics/visualisation/rendering.html">1f: Rendering</a></li>
<li><a href="$rootdir$/dynamics/visualisation/movies.html">1g: Movies</a></li>
<li><a href="$rootdir$/dynamics/visualisation/picking.html">1h: Picking Atoms</a></li>
<li><a href="$rootdir$/dynamics/visualisation/comparing.html">1i: Comparing Trajectories</a></li>
<li><a href="$rootdir$/dynamics/visualisation/whatnext.html">1j: What Next?</a></li>
</ul>
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<li><a href="$rootdir$/dynamics/dynamics/README.html">Part 2: Molecular Dynamics</a>
<ul>
<li><a href="$rootdir$/dynamics/dynamics/getting_started.html">2a: Getting Started</a></li>
<li><a href="$rootdir$/dynamics/dynamics/theory.html">2b: Theory of MD</a></li>
<li><a href="$rootdir$/dynamics/dynamics/time.html">2c: Changing Time</a></li>
<li><a href="$rootdir$/dynamics/dynamics/shake.html">2d: Shake (Rattle and Roll)</a></li>
<li><a href="$rootdir$/dynamics/dynamics/protein.html">2e: Periodic Boundary Conditions</a></li>
<li><a href="$rootdir$/dynamics/dynamics/pressure.html">2f: Under Pressure</a></li>
<li><a href="$rootdir$/dynamics/dynamics/simulation.html">2g: Running the Simulation</a></li>
<li><a href="$rootdir$/dynamics/dynamics/whatnext.html">2h: What Next?</a></li>
</ul>
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<li><a href="$rootdir$/dynamics/mutation/README.html">Part 3: Mutation Studies</a>
<ul>
<li><a href="$rootdir$/dynamics/mutation/gettingstarted.html">3a: Getting Started</a></li>
<li><a href="$rootdir$/dynamics/mutation/mutation.html">3b: Mutating the Protein</a></li>
<li><a href="$rootdir$/dynamics/mutation/solvation.html">3c: Solvating the Protein</a></li>
<li><a href="$rootdir$/dynamics/mutation/minimisation.html">3d: Minimising the System</a></li>
<li><a href="$rootdir$/dynamics/mutation/heating.html">3e: Heating the System</a></li>
<li><a href="$rootdir$/dynamics/mutation/equilibration.html">3f: Equilibrating the System</a></li>
<li><a href="$rootdir$/dynamics/mutation/simulation.html">3g: Running the Simulation</a></li>
<li><a href="$rootdir$/dynamics/mutation/compare.html">3h: Comparing Trajectories</a></li>
<li><a href="$rootdir$/dynamics/mutation/whatnext.html">3i: What Next?</a></li>
</ul>
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</ul>
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<li><a href="//chryswoods.com/embo2014/Practical.html">QM/MM Monte Carlo</a></li>
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<li><a href="$rootdir$/main/softwarecarpentry.html">Software Carpentry</a>
<ul>
<li><a href="http://tinyurl.com/swcbath">Bath (July 2013) Workshop</a></li>
<li><a href="http://tinyurl.com/swcbristol">Bristol (September 2013) Workshop</a></li>
<li><a href="http://tinyurl.com/swcexeter">Exeter (November 2013) Workshop</a></li>
</ul>
</li>
</ul>
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<li><a href="$rootdir$/main/software.html">Software</a>
<ul>
<li><a href="//siremol.org">Sire Molecular Simulation Framework</a></li>
<li><a href="http://protoms.org">ProtoMS Monte Carlo Package</a></li>
</ul>
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<li><a href="$rootdir$/main/publications.html">Publications</a></li>
<li><a href="$rootdir$/talks/README.html">Talks</a></li>
<li><a href="$rootdir$/main/links.html">Useful Links</a></li>
<li><a href="$rootdir$/main/reading.html">Books that are Worth Reading</a></li>
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