Thompson Group Reference Documentation

About this manual and other important links

This documentation covers a variety of topics, including (but not limited to): Getting access to the KU Community Cluster, PyMOL, PACKMOL, and more. Please see the Contents section below for all available tutorials on the site. Other important links are shown below.

Contents

• Joining the KU Community Cluster
  • Applying for a Cluster Profile
  • Connecting to the Cluster off Campus with KUAnywhere
• Basic Terminal Commands
  • Navigating Directories
  • Efficient Typing in the Terminal
  • Editing Files
  • Copying and Removing
  • Other Helpful Commands
• Cluster Commands
  • Basic Commands
  • Modules on the Cluster
  • Editing Your .bash_profile
  • Creating Alias Commands
    • When off the Cluster
    • When on the Cluster
• PyMOL
  • Installation
  • Basics: GUI
    • Opening a Trajectory
    • Working with an Object
    • Common Commands
    • Saving Images
    • Scripting
• VMD (Visual Molecular Dynamics)
  • VMD Basics
    • Graphics
    • Recommended Links
• GitHub
  • Syncing a VS Code Remote SSH Workspace with GitHub
    • 1. Verify Git Is Available on the Cluster
    • 2. Navigate to Your Project Directory
    • 3. Configure Git (First Time Only)
    • 4. Create a GitHub Repository
    • 5. Set Up SSH Authentication
    • 6. Add the SSH Key to GitHub
    • 7. Test GitHub Authentication
    • 8. Connect the Local Repository to GitHub
    • 9. Create a .gitignore File
    • 10. Add Files
    • 11. Commit Changes
    • 12. Push to GitHub
    • Troubleshooting: “Can’t push refs to remote”
    • Daily Workflow
    • Helpful commands
• PACKMOL
  • Installing PACKMOL
  • Preparing the PACKMOL Contents
  • Running PACKMOL
  • Examples
    • TIP3P-FB Water Model
      • Connect File
      • Bond Coefficients File
    • Methylurea Model
      • Connect File
      • Angle Coefficiens File
      • Dihedral Coefficients File
• MOLDEN
  • Reading Files and Editing the Z-Matrix
    • Z-Matrix Basics
    • Creating, Editing, and Optimizing Structures
    • Saving Z-Matrices and Coordinates
• Developing Molecules for LAMMPS
  • Obtaining Force Field Data
    • CGenFF Example
  • Creating the Molecule
    • Implementing Force Field Data
      • PACKMOL Steps
    • Optimizing the Structure with LAMMPS
      • LAMMPS Steps
      • LAMMPS Energy Minimization Header Example
      • LAMMPS Energy Minimization Footer Example
      • LAMMPS Energy Minimization File Example
      • LAMMPS Energy Minimization Bash Script Example
      • Troubleshooting Energy Minimization
      • Importing Optimized Geometry to PACKMOL
  • Other LAMMPS Tips
• Monthly Status Report (MSR)
  • Content
  • Mechanics
  • Semester Status Reports (SSR)
• Other Resources
  • Poster Templates and Examples

Other Important Links

• Thompson Group Website: https://thompsongroup.ku.edu

• LAMMPS Documentation: https://docs.lammps.org/

• KU Cluster Wiki: https://help.ittc.ku.edu/clusterdocs/

• American Chemical Society Website: https://www.acs.org

Note

This project is under active development.