gromacs_replicate_traj_analysis

Description: A system with 5 replicates analyzed using GROMACS. This folder contains scripts to concatenate and analyze trajectories for each replicate, followed by plotting all replicates together for comparison and visualization.

Molecular Dynamics (MD) Trajectory Analysis Workflow

This workflow automates post-processing and analysis of MD simulations for 5 replicates (you can many multiple replicates) of a protein-ligand system (likely a membrane protein with transmembrane domains).

shwetam0302@gmail.com

Directory Structure

./ ├── replicate1/ │ ├── ana1.sh # Analysis script for replicate 1 │ ├── replicate1*.xtc # Raw trajectory files (e.g., replicate1.xtc, replicate1.part0002.xtc) │ ├── replicate1.tpr # Topology/run input file │ ├── index.ndx # GROMACS index file with custom groups │ └── sim_ana/ # Analysis output directory │ ├── sasa/ # Solvent accessible surface area results │ └── tm_rmsd/ # Transmembrane domain RMSD results └── ... (replicate2-5 with similar structure)

Step 1: Generate Concatenation Scripts

bash concat_traj.sh

About: Automatically generates trajectory concatenation scripts for each replicate system (1-5).

Key Features Replicate-Specific Control: Creates individual concat_{i}.sh scripts in each replicate folder Safety First: Leaves original trajectory files untouched Customizable: Easily modify for different numbers of replicates or trajectory patterns

Output Structure replicate1/ └── concat_1.sh replicate2/ └── concat_2.sh ... replicate5/ └── concat_5.sh

Usage Tips Edit concat_traj.sh to: Change number of replicates ({1..5} → {1..N}) Modify trajectory filename patterns (trajout*xtc) Target specific replicates (e.g., 2 4 5 instead of all)

Step 2: Execute Concatenation & Organize Files

Execution Options

Default sequential processing

bash run_concat_traj.sh

Parallel processing (requires GNU Parallel)

find . -name "concat_*.sh" | parallel -j 2

What It Does

• Concatenates Trajectories

  • Processes replicates sequentially
  • Merges split trajectory files (e.g., replicate1.xtc, replicate1.part0002.xtc) into single trajectories

• Centralizes Essential Files

• Copies these files to each replicate folder:

  • input.pdb (initial structure)
  • input.tpr (topology/parameters) keep only necessary files for analysis

Step 3: Generate System Index File

bash makeIndex.sh

Key Features

• Centralized Indexing: Creates index_replicate.ndx in the project root folder
• Cross-Replicate Compatibility: Shared by all replicate systems (1-5)
• Reproducible Selection: Uses EOD blocks to document atom/residue choicest for other system as well change the atom/residue index

Step 4: Generate Analysis Scripts (ana[1-5].sh)

bash create_analysis.sh

Creates individual ana{i}.sh scripts in each replicate folder

Step 5: Run Analysis Scripts (ana[1-5].sh)

bash run_analysis.sh

Per-replicate scripts performing:

• Trajectory Processing

  • System centering and PBC correction
  • Alignment to reference structures (TM domains)

• Quantitative Analysis

  • RMSD calculations (backbone, TM domains, ligand)
  • RMSF (residue flexibility)
  • SASA (solvent accessibility)
  • Distance measurements (key residue pairs)

Output Files Processed Trajectories

no_pbc_*.xtc - PBC-corrected trajectory

aligned_no_pbc.xtc - Aligned trajectories

Analysis Results

*.xvg - GROMACS analysis data files (plottable with Grace/Xmgrace)

*.pdb - Representative structures (initial/final frames)

Step 6: Plot the data

1. rmsf_all_rep_protein_ligand.ipynb

   • Plots the Root Mean Square Fluctuation (RMSF) for protein and ligand across all replicates from gromacs output .xvg files.

2. rmsd_all_rep.ipynb

   • Plot the Root Mean Square Deviation (RMSD) for all replicates from gromacs output .xvg files.

3. combined_all_rep_density_plot.ipynb

   • Combines data from all replicates and plots a density distribution for the combined dataset from gromacs output .xvg files.

4. replicate_wise_density_plot_from_xvg.ipynb

   • Generates density plots for each replicate individually using data from .xvg files.

5. mindist_plot_all_rep.ipynb

   • Plots the minimum distance for all replicates from gromacs output .xvg files.