TriplexDynamiX

Welcome to TriplexDynamiX, My molecular dynamics application designed for trajectory analysis, energy minimization, and comprehensive data handling and interpretation. I am continually developing more features to enhance its functionality. Originally focused on analyzing RNA triple stability, TriplexDynamiX serves as an excellent starting point for researchers new to molecular dynamics. For additional applications, please refer to the OpenMM and MDtraj documentation.

How to Use TriplexDynamiX:

1. Clone the repository:

   git clone https://github.com/Yusuprozimemet/MolecularDynamicsApp.git
   

2. Set up a Python 3.7 environment:

   conda create -n yourenv python=3.7
   

3. Activate your environment:

   conda activate yourenv
   

4. Update your environment:

   conda env update -n yourenv -f environment.yaml
   

5. Place your input PDB files in src/MolecularDynamics/data/input. Ensure these files are prepared for molecular dynamics simulations. Results will be found in src/MolecularDynamics/data/output.

6. Navigate to the appropriate directory to run your desired Python script.

7. Customize parameters in the YAML files for the scripts.

8. For questions or issues, please contact with me.

Enjoy using TriplexDynamiX!