Course on molecular dynamics, 1st yr masters in Physical Sciences - Sciences de la Matière, ENS de Lyon.
TODO add detailed comments to in.lmp
The case studies below make use of Python libraries and simulation codes installed in the machines of the Centre Blaise Pascal, CBP.
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.
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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)
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VMD: /usr/local/bin/vmd (in the PATH)
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Avogadro: /usr/bin/avogadro (in the PATH)
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Open Babel: /usr/bin/obabel (in the PATH)
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Gromacs: /usr/bin/gmx (in the PATH)
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OpenMM, mdtraj: in the
ommconda environmentconda activate omm
ljatoms-- simple MD code for Lennard-Jones atomsljmols-- simple MD code for 2-site Lennard-Jones moleculeswater-- simulation of water using LAMMPSsolvation-- simulation of solvation of NaCl and ethelene glycol in water using LAMMPS
Utilities to plot LAMMPS output from `log.lammps, to display the simulation box using VMD, etc.