Tutorials
  1. Linux tutorial
  2. Mathematica Tutorial from the Milner Group at Penn State
  3. GROMACS Manual 
  4. GROMACS Tutorial from the Milner Group at Penn State
  5. GROMACS Tutorial from the Lemkul Group at Virgia Tech
  6. How to submit jobs to the Discovery Cluster: CPU jobs, GPU jobs
  7. LAMMPS Manual
Softwares and Tools
Tools for generating initial configurations and topology files for simulations
  1. Avogadro
  2. Packmol
  3. Moltemplate
  4. CHARMM-GUI
  5. United-Atom TraPPE
Simulation packages
  1. GROMACS
  2. LAMMPS
  3. HOOMD-blue
  4. Gaussian and GaussView
Visualization tool
  1. VMD
Free energy sampling tools
  1. PLUMED
  2. WHAM
Chemical Databases
  1. Virtual Chemistry
  2. NIST Chemistry WebBook
Writing tools
  1. Latex
  2. Overleaf for Latex