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.hf1.

Start with the Tutorial.

If you use gRINN for research or commercial purposes, please cite the following publication of gRINN in your publication (article, thesis, etc.):

[SO201]

Onur Serçinoğlu, Pemra Ozbek; gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W554–W562, https://doi.org/10.1093/nar/gky381

News

2018/11/27: Thank you for your interest in gRINN! We greatly appreciate your feedback. We’re aware of several bugs, including incompatibility with some input data and gromacs versions, We’re currently working to fix them in the next version release (anticipated January 2019). If you also experience problems, please feel free to send an email to onursercin AT gmail DOT com!

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
  • Preparing NAMD/CHARMM input data for gRINN
    • Deleting non-protein atoms from PSF/PDB files
    • Deleting non-protein atoms from DCD trajectory files
    • (Re)-assigning chain IDs back to the PDB file
  • Deleting non-protein atoms from GROMACS input data
    • Deleting non-protein atoms from TOP files
    • Deleting non-protein atoms from TPR files
• Issues and History/Change Log
  • Known Issues - To-do List
    • Planned features/fixes (short-term)
    • Planned features/fixes (longer-term)
    • Planned features/fixes (unlikely to implement in foreseeable future)
  • v1.1.0.hf1 (2018/06/21)
  • v1.1.0 (2018/04/06)
  • v1.0.1 (2017/12/27)
• FAQ
• Credits
• Citing gRINN
• Source Code
• 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