MD

Course on molecular dynamics, 1st yr masters in Physical Sciences - Sciences de la Matière, ENS de Lyon.

Working environment and codes

The case studies below make use of Python libraries and simulation codes installed on the machines of the Centre Blaise Pascal, CBP.

Python environment

A conda installation with the simulation codes and tools is installed in /projects/DepartementChimie/miniforge3. To activate it append the contents of the conda.rc file (in the utils folder) to your .bashrc and then login again. The base environment contains jupyter, numpy, matplolib, etc.

Paths to codes on the CBP

• OpenMM, mdtraj: available in the openmm conda environment

    source /projects/DepartementChimie/conda.rc
  

(you can add the contents of this file to your .bashrc)

    conda activate openmm

• fftool: /projects/DepartementChimie/fftool

    export PATH=/projects/DepartementChimie/fftool:$PATH
  

(you can add this line to your .bashrc)

• packmol: /usr/bin/packmol (in the default PATH)
• VMD: /usr/local/bin/vmd (in the default PATH)
• Avogadro: /usr/bin/avogadro (in the default PATH)
• VESTA: /usr/local/bin/VESTA (in the default PATH)
• Open Babel: /usr/bin/obabel (in the default PATH)

GPU

To check your machine's GPU configuration and monitor its usage:

    nvidia-smi

You can select and see the state of the CBP machines on the Cloud@CBP web page.

Study cases

• ljatoms -- simple MD code for Lennard-Jones atoms
• ljmols -- simple MD code for 2-site Lennard-Jones molecules
• openmm_basic -- basic simulation using OpenMM (water)
• ionicliquid -- a room-temperature molten salt
• solvation -- solvation of simple ions and molecules
• surface -- graphene and graphite surfaces

Utilities

Utilities to improve visualization using VMD, print auxilliary quantities, etc.