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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 in the machines of the Centre Blaise Pascal, CBP.

Python environment

A conda installation with the simulation codes and tools is installed in /projects/DepartementChimie/miniconda3. 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

  • LAMMPS: /projects/DepartementChimie/lammps/bin/lmp

    Include in your .bashrc (and then restart a terminal shell):

      DEPT=/projects/DepartementChimie
  export LD_LIBRARY_PATH=$DEPT/plumed/lib
  export PATH=$DEPT/lammps/bin:$PATH

  • packmol: /usr/bin/packmol (in the PATH)

  • VMD: /usr/local/bin/vmd (in the PATH)

  • Avogadro: /usr/bin/avogadro (in the PATH)

  • Open Babel: /usr/bin/obabel (in the PATH)

  • Gromacs: /usr/bin/gmx (in the PATH)

  • OpenMM, mdtraj: in the omm conda environment

      conda activate omm

Study cases

  • ljatoms -- simple MD code for Lennard-Jones atoms
  • ljmols -- simple MD code for 2-site Lennard-Jones molecules
  • water -- simulation of water using LAMMPS
  • solvation -- simulation of solvation of NaCl and ethelene glycol in water using LAMMPS

Utilities

Utilities to plot LAMMPS output from `log.lammps, to display the simulation box using VMD, etc.