MD-Tutorials

Tutorials on the basics of molecular dynamics, including:

1. Setting up a system from scratch in LAMMPS: C2M-TF2-lmp

   • Pack an ionic liquid system (C2M-TF2) using packmol
   • Generate .lt files given the pdb file of each of the system components
   • How to specify a forcefield for the system

2. Setting up a GAFF system from scratch in GROMACS: C2M-TF2-gro

   • Pack an ionic liquid system (C2M-TF2) using packmol
   • Generate coordinate .gro and topology .top files for the system given the pdb file of each component