Welcome to gRINN’s documentation!

gRINN is a software for residue interaction enery-based analysis of protein MD simulation trajectories.

Current version is v1.1.0.

Start with the Tutorial.

Contents:

• Introduction
• Obtaining gRINN
  • Dependencies
    • Obtaining NAMD
    • Obtaining GROMACS
  • Download gRINN
  • Starting the application
• Tutorial
  • Preparing input data
    • For NAMD/CHARMM-generated trajectories
    • For GROMACS-generated trajectories
  • Starting the Application
  • gRINN Main Window
  • gRINN New Calculation
    • Input files, output folder and NAMD/GMX executable paths
    • Calculation settings
    • Correlation settings
    • Starting and monitoring the calculation
    • Start calculation with sample NAMD data
  • gRINN View Results
    • Pairwise Energies
    • Interaction Energy Matrix
    • Interaction Energy Correlations
    • Residue Correlation Matrix
    • Network Analysis
    • References
    • Output folder content
  • gRINN with GROMACS data
  • gRINN Command-Line Interface
• Miscellaneous
  • Deleting non-protein atoms from NAMD/CHARMM input data
    • Deleting non-protein atoms from PSF/PDB files
    • Deleting non-protein atoms from DCD trajectory files
  • Deleting non-protein atoms from GROMACS input data
    • Deleting non-protein atoms from TOP files
    • Deleting non-protein atoms from TPR files
• History/Change Log
• FAQ
• Credits
• Contact
• License
  • License Grant
    • You are not permitted to:
  • Third-party tools included in gRINN:
  • Intellectual Property and Ownership
  • Termination
  • Governing Law

Indices and tables

• Index
• Module Index
• Search Page