This repository contains two laboratory exercises in relationship to the topic of molecular dynamics as a part of the course Statistical Thermodynamics and Molecular Simulation (KEMM38) 2021.
To open the Notebooks, we consider two options. 1. The usage of Binder (recommended). 2. Running the Notebook on your local computer.
To open the Notebooks in Binder, simply click the Binder shield/URL in the top of the document or by clicking here.
To open the Notebooks, install Python3 via Miniconda or Anaconda, and make sure all required packages are loaded using the following terminal commands
conda env create -f environment.yml
source activate MD_lab
jupyter-notebookThis will open the Jupyter Notebook Folder with the root being the folder you executed the previous commands. In Jupyter open a new terminal and execute the command ./postBuild installing the molecular dynamics software and enabling Jupyter widgets.
Part1_BarrierCrossing.ipynbJupyter Notebook to perform 1D molecular dynamics simulations using Python and generate plots.Part2_Diffusion.ipynbJupyter Notebook to perform 3D molecular dynamics simulations using in-house software and generate plots.include/Folder containing premade data, figures and images.MolecularOverkillEngine/In-house developed molecular dynamics software.figures/Folder containing figures generated from the Jupyter Notebooks.dataFolder containing start configurations, force field files and software input.
Each student is expected to hand in a written report based on the two labs with the grades passed or not-passed. The written report is to be handed in no later than Tue 23/03 23:59 with the posibility of handing in a first draft no later than Fri 05/03 23:59 and recive comments no later than Fri 12/03. The report may be submitted via Canvas or email to the lab responsibles.
If you have any questions, you can contact the lab responsibles on the following electronic addresses
stefan.hervo_hansen@teokem.lu.se
vidar.aspelin@teokem.lu.se
samuel.stenberg@teokem.lu.se