Lecture3
Section outline
-
Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient
Video 1: Solvation of 10 ethane molecules using a water box is shown. The process is done by using the GUI of VMD and a home-made TCL code. A glimpse of ionization (adding salt) is also demonstrated.
Video 2: After scrutinizing the configuration file, the MD simulation of ethane molecules is visualized in VMD. Periodic boundary conditions (PBC) and Langevin temperature/pressure control are briefly mentioned.
Wikipedia pages for PBC and Langevin dynamics are informative:
https://en.wikipedia.org/wiki/Periodic_boundary_conditions
https://en.wikipedia.org/wiki/Langevin_dynamics
Video 3: The diffusion coefficient and heat capacity are computed using a Jupyter notebook. Mean squared deviation (MSD) is used for the calculation of the diffusion coefficient.For the relation of slope and diffusion please see:
https://mathbench.umd.edu/modules/cell-processes_diffusion/page10.htm
A good random walk guide:
https://en.wikipedia.org/wiki/Random_walk
Nevertheless, for heat capacity:
https://en.wikipedia.org/wiki/Heat_capacity
Video 4: Advanced visualization in VMD is demonstrated using the MD of ethane molecules.
-