Resources

Simulation

• Visualization
  • Visual Molecular Dynamics (VMD)
  • Ovito
• Simulation Preparation
  • Packmol
• Molecular Dynamics Force Fields
  • LigParGen: OPLS Force Field
  • TraPPE Force Field
• Simulation Software
  • Gaussian
  • Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
  • Gromacs
  • ESPResSo++
  • HooMD Blue

Programming

• Python
  • Anaconda: Jupyter Notebook
  • Basic tutorial
  • Pandas: Good data management
  • Scikit-Learn: Basic machine learning
• C++ tutorial
• Fortran tutorial
• Parallel programming
  • OpenMP
  • MPI

Writing, Presentation, and Figure-Making

• Software
  • Matplotlib: Python library for creating publication-ready figures
  • Inkscape: Arrange data and graphics into coherent figures
  • Mendeley: Citation manager
  • Texmaker: LaTeΧ editor
  • Overleaf: Cloud-based LaTeΧ editor
• Guides and tips
  • Overview of the writing, presentation, and figure-making process
  • Figure-making tips with specific examples using Inkscape
  • Another perspective on writing
  • Additional presentation tips

Career Planning

• MyIDP: Career-planning tool from American Association for the Advancement of Science
• ChemIDP: Career-planning tool for chemical scientists from the American Chemical Society
• Versatile PhD: For PhD scientists interested in non-academic careers. Requires UT EID for full access.