Welcome to CSU-wiki's Documentation!

Thanks for visiting the CSU Theory Suite's wiki page! Feel free to also visit the Paton Lab Website or the Kim Lab Website!

Adding Packages

• Adding Pages to the Wiki
  • 1. Fork the Repository
  • 2. Clone Your Fork to Your Computer
  • 3. Ensure Your Environment is Adequate
  • 4. Generate a Local Preview of Existing Files
  • 5. Make Modifications in RST Files
  • 6. Save Your Changes to the RST Files
  • 7. Pushing Results to Your Personal GitHub Fork
  • 8. Creating a Pull Request

Getting Started

• Paton Lab Computing Resources
  • Expanse and Bridges2
  • Alpine
  • ACME
  • Local Resources
  • RStor File Storage
• Kim Lab Computing Resources
  • Alpine
  • ACME
  • Local Resources
• Essential Unix Commands
• File System Layout
  • Root Directory
  • Bin Directories
  • Home Directory
• Submitting Jobs
  • Halting and Canceling Interactive Processes
  • Running in Background vs Foreground, and nohup
  • Listing and Killing Jobs Running in Background
  • Using a SLURM Queueing Manager
• Fun with Coworkers
  • Send a Message to All Users' Terminal Windows
  • Send a Message to a User's Terminal Window
• Coding Resources
  • Python
  • Bash
• Working with Files
  • touch - Crating an Empty File
  • vi - Reading and Writing in the Terminal
  • Reading File Contents
  • sed - Editing Files in the Command Line
  • Condensing Files/Folders
  • Looking for Patterns
  • sort - Sorting and Re-Ordering Data
• Moving/Renaming Files
  • mv - Changing a File Name or Location
  • rename - Changing the Name of Many Files in the Same Way
  • cp - Copying a File to a New Location
  • Moving Only Certain Files
  • Copying/Transferring to a New Computer
• Terminal Basics
  • Using Wild Cards
  • Navigating Folders
  • Redirecting Output to a File
  • Creating Shortcuts for Common Commands
  • Clearing the Terminal Screen
  • Search Previous Commands
  • Display a Line of Text
  • How to Logout
  • Auto Fill Unique Names
  • Listing Files
  • Canceling a Command Before you Execute
  • Back to the Beginning of the Command Prompt
  • Combining Commands into a Single Line
• Working with Computers
  • What Computer am I Working on?
  • Remotely Accessing Computers or Clusters
  • Who am I Logged In As?
  • What Processes are Running in my Terminal Window
  • Learn About the Computer
  • which - What Program am I Using?
  • Disk Usage Details
  • Search for Files
  • Tell the Computer to Wait
• Using GitHub
  • Saving Work/Progress with GitHub

Helpful Packages

• GoodVibes
• DBSTEP
• REGGAE
• DISCO
• AQME
• Slurm Job Tracking
• pyssian
• RDKit
• CREST
• ROBERT
• YADDA

Graphical Software

• Inkscape & GIMP
  • Installation
    • Inkscape
    • GIMP
  • Inkscape Basics
    • Creating a path
    • Alignment
    • Changing-selecting colors
    • Creating gradients
    • Path effects
    • Clipping
    • Exporting to png
  • Combining Inkscape and GIMP
• Matplotlib
  • Basics
    • Simplest usage
    • Figure, Axes, Gridspec and kwargs
    • Plot types ( .plot, .scatter, .imgshow, .bar, … )
    • Changing axes properties and cheatsheets
    • Colors and creating a custom colormap
• PyMOL
  • Installation
    • Linux
  • Pymol Basics
    • Basic controls
    • Basic commands
    • PyMOL Scripts and Command Line Rendering
    • Standard Group Designs

Example Workflows

• End-to-End Workflow in ACME
  • 1. Activating the conda environment
  • 2. Using OpenBabel
  • 3. Running an XTB calculation
  • 4. Running a CREST calculation
  • 5. Running a CENSO calculation
  • 6. Running QM calculations. Gaussian, ORCA, AQME and Goodvibes
• GoodVibes
  • Installation
  • Computing Thermochemistry for QM Output Files
  • Temperature Corrections
  • Quasi-Harmonic Corrections
  • Single Point Calculations
  • Potential Energy Surface Calculations:
  • Putting it All Together
• REGGAE
  • Installation
  • Example 1: Performing a multivariate regression
  • Example 2: Performing a multivariate regression
  • Regression Plot Generated
  • Pearson Correlation Plot
  • Diagnostics Plot
  • PCA Plot
• RDKit, Mordred, Morfeus & DBStep
  • Installation
  • Dependencies
  • Example notebook
    • RDKit: a cheminformatics package
      • Step 1: 2D smiles to 3D structure
      • Step 2: RDKit for molecular, atomic and bond properties
      • Step 3: Other RDkit Descriptors
      • Step 4: Substructure matching
      • Step 5: Chemical transformations
      • Step 6: Atom/Bond deletion/addition
    • Modred: a descriptors package
    • Morfeus: a descriptors package
    • DBstep: a descriptors package
• CENSO
  • Getting Started
    • Generate Structure from smiles
    • Performing a Quick Optimization
  • Performing a CREST Conformation Search
  • Initial Sorting with CREGEN
  • Running CENSO
  • Final Sorting
• NCIPLOT
  • Running the NCIPLOT calculation
    • 1. Prepare basic files
      • if we want to use pure xyz
      • if we want to use wfn
    • 2. Prepare the nci input file
    • 3. Run nciplot
    • 4. Plot the results
    • 5. Examples
  • Plotting in Pymol
    • 1. Prepare the files
    • 2. Starting Pymol
    • 3. Loading the geometry
    • 4. Start making things pretty
    • 5. Loading the density and gradient
    • 6. plotting the NCI
    • 7. Basics of visualization
    • 8. Generating a nice image
    • 9. Generating image layers for composition
• qcalibrate
  • qcalibrate Processes
    • Step 1: Modredundant Optimization
    • Step 2: Constrained CREST Search
    • Step 3: Constrained Optimization
    • Step 4: Unrestrained Transition State Optimization
  • Set-up
  • Running the Code
    • Frequency Cutoff
    • Wall Time
    • Number of Processors
    • Number of Conformers
• YADDA
  • Installation
  • Preparation
    • IRC Output File
    • Example Input File
    • YADDA Input File
    • (optional) Optimized Reactant Files
  • ALMO-EDA Calculations
  • QM Calculations
  • ONIOM-EDA Calculations

Concepts

• Classical Molecular Dynamics
  • Understanding the Basics
  • Step 1: Prepare System
  • Step 2: Minimization
  • Step 3: Heating
  • Step 4: Equilibration
  • Step 5: Production