In this part of the course, you will be able to set up a model of the system of your choice. I provide input files to create and set up systems used in my publications and work:

  1. Amino acids and layered double hydroxides – the study of the prebiotic formation of protobiomolecules.
  2. Crude oil components and silicate clays – the study of the effect of soils for the enhanced oil recovery (EOR).
  1. Graphene sheet and crude oil – the study of the effect of asphaltenes deposition on EOR (Thank you Shansi Thian for providing data and notes).
  2. Zwitterionic glyphosate molecules and silicate clays – the study of the interactions of herbicides and soils.
  3. Dynamics withing diamantane crystal – the study of the relation between SS-NMR and MD for the understanding of dynamics in solids.

Please NOTE, since some of the work has not been published yet, set up for systems are available on request.


This practical will span over two sessions, in the first session we will construct the system and submit to run on the HPC. The week between will provide enough time to complete simulation and analyse data. We will spend the second session finishing analysis, plotting data and discussing results.