GROMACS Trajectory Analysis Tutorial

This repository contains a step-by-step tutorial for analyzing molecular dynamics (MD) simulations using GROMACS.

---

MD simulation analysis can be categorized into three main groups:

1. Essential Structural Analysis:

These methods provide insights into the structural changes and stability of the system throughout the simulation. They help in understanding how the structure of the molecule changes over time.

1. Root Mean Square Deviation (RMSD): Measures the average distance between the atoms of superimposed proteins.
2. Root Mean Square Fluctuation (RMSF): Determines the flexibility of different parts of a protein structure.
3. Radius of Gyration (ROG/Rg): This gives an idea about the compactness of the protein structure during the simulation.
4. Hydrogen-bond Analysis (HBond): Provides insights into the stability of the protein structure.
5. Solvent Accessible Surface Areas (SASA): Calculates the exposure of the protein to the solvent.
6. Secondary Structure Element (SSE) Analysis: Provides information about the secondary structure elements of the protein during the simulation.

2. Essential Dynamic Analysis:

These methods provide insights into the system's dynamic behaviour. They help to understand the movements and interactions of the molecule.

1. Principal Component Analysis (PCA).
2. Porcupine plot analysis of PCA.
3. Clustering analysis.

3. Binding free energy analysis

1. MM-PB(GB)SA
2. Decomposition

The tutorial covers the following steps:

1. Making Directory and Linking Required Files

Create a new directory for analysis and link the required files from the parent directory.

2. Cleaning Trajectory and Extracting First Frame

Clean the trajectory and extract the first frame using gmx trjconv.

3. RMSD, RMSF, ROG/Rg, SASA and SSE

Calculate the Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of Gyration (Rg/ROG) using gmx rms, gmx rmsf, gmx gyrate, gmx sasa and gmx do_dssp respectively.

4. PCA

1. Perform Principal Component Analysis (PCA) using the pca.py script from the MODE-TASK tool.
2. Comparing PCA results from two different trajectories (Will be updated soon).

5. Clustering

Perform clustering to group similar structures from a trajectory using the ttclust tool.

6. MMPBSA

Calculate the binding free energy of a system using the gmx_MMPBSA tool.

---

Detailed instructions and comments for each step are in the tutorial script file.

Feel free to ask if you have any more questions or need more help.

Happy simulating! 😊.