Protein-Simulation-Pipeline

This repository provides a comprehensive and structured workflow to perform molecular dynamics (MD) simulations of proteins using GROMACS. The pipeline begins with protein structure preparation and proceeds through solvation, energy minimization, equilibration phases (NVT and NPT), production MD run, and ends with essential post-simulation analyses.

This setup is intended for researchers working on protein stability, folding, or interaction studies, and is adaptable to a range of simulation conditions with appropriate .mdp configuration files.

Requirements

• GROMACS (2020 or later recommended) installed and sourced properly
• Input protein structure file in PDB format: Protein.pdb
• Simulation parameter files: ions.mdp, minim.mdp, nvt.mdp, npt.mdp, md.mdp
• Optional: xmgrace or any other .xvg file plotting tool for visualization

Workflow Overview

1. Environment Setup

source /usr/local/gromacs/bin/GMXRC
gmx

2. Structure Preparation

• Remove crystallographic water molecules
• Generate topology and initial coordinate files using a selected force field (e.g., OPLS-AA)

grep -v HOH Protein.pdb > clean.pdb
gmx pdb2gmx -f clean.pdb -o protein.gro -water spce -ignh

3. Define Simulation Box and Solvate

gmx editconf -f protein.gro -o box.gro -c -d 1.0 -bt cubic
gmx solvate -cp box.gro -cs spc216.gro -o solv.gro -p topol.top

4. Add Ions to Neutralize the System

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

5. Energy Minimization

gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

6. Equilibration

• NVT (Constant Volume and Temperature)

gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -deffnm nvt
gmx energy -f nvt.edr -o temperature.xvg

• NPT (Constant Pressure and Temperature)

gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -deffnm npt
gmx energy -f npt.edr -o pressure.xvg
gmx energy -f npt.edr -o density.xvg

7. Production MD Run

gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md.tpr
gmx mdrun -deffnm md

Post-Simulation Analysis

Trajectory Processing and Analysis

• Remove periodic boundary artifacts and center molecule:

gmx trjconv -s md.tpr -f md.xtc -o md_noPBC.xtc -pbc mol -center

RMSD and RMSF Analysis

gmx rms -s md.tpr -f md_noPBC.xtc -o rmsd.xvg -tu ns
gmx rmsf -s md.tpr -f md_noPBC.xtc -o rmsf.xvg -res

Radius of Gyration

gmx gyrate -s md.tpr -f md_noPBC.xtc -o gyrate.xvg

Output Summary

File	Description
*.gro, topol.top	Coordinate and topology files
*.tpr, *.cpt, *.edr	Run input and output files
*.xvg	Energy and analysis output for plotting
All intermediate and final results are saved step-by-step to maintain reproducibility and traceability.

Notes

Ensure the .mdp files used for each phase are appropriately tuned to your simulation system. For high-throughput runs or automated setups, consider integrating the pipeline into a shell script or workflow manager.

Maintainer

• Sourabh Kumar bioinfosourabh@gmail.com
• This repository is open for contributions, issues, and suggestions to enhance utility for the molecular simulation community.