GROMACS Tutorial - Introduction, Procedure & Data Analysis

Introduction, Detailed Procedure and Data Analysis of Molecular Dynamics Simulations Using GROMACS

1. Molecular Dynamics Simulations with GROMACS By: M ayur Mukhi , WATER Lab., SSSIHL, PSN Campus

2. Components Introduction Procedure Data Analysis

3. Introduction What is MD Simulations? Computer programs that simulate the atomic behavior of molecules to mimic the real-life physical forces that they experience. Why do MD Simulations? To bring the molecule to a natural (physiological) and dynamic system. Assess stability and structural compactness

4. Things to note 1. .MDP files are parameter files 2. .TPR are prerequisite files 3. .GRO is a protein file format 4. You can play around with GROMACS

5. Procedure (using Ubuntu terminal)

6. 1. Protein Preparation Preparing the Protein Protein Processing (Without Heteroatoms) Selecting Force Field Selecting Water Model Commands: gmx pdb2gmx -f protein.pdb -o protein_processed.gro Calling the program Module Input Output Outputs Topology File ( topol.top ) Position Restraint file ( posre.itp ) p rotein_processed.gro

7. 2. Solvating the system Solvation Creating a box Adding Water Commands: gmx editconf -f protein_processed.gro -o newbox.gro - bt cubic -d 1.0 (Creating Box) gmx solvate - cp newbox.gro - cs spc216.gro -p topol.top -o solv.gro (Adding Water) Shape Size Outputs Newbox.gro Solv.gro

8. 3. Adding ions Commands: 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 Outputs Ions.tpr solv_ions.gro

9. Solvated protein with ions

10. 4. Energy Minimization To obtain the lowest energy conformation of the protein in the particular system Commands: gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em Outputs em.tpr em.gro

11. 5a. Equilibration - nvt Constant number of molecules (N), volume (V) and Temperature (T) – NVT Commands: gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr gmx mdrun -v -deffnm nvt Outputs Nvt.tpr Nvt.gro Nvt.cpt

12. 5b. Equilibration - npt Constant number of molecules (N), Pressure (P) and Temperature (T) – NPT Commands: gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -o npt.tpr gmx mdrun -v -deffnm npt Outputs Npt.tpr Npt.gro Npt.ctp

13. 6. Final Md run Constant temperature and pressure for a particular amount of time Commands: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_30.tpr gmx mdrun -v -deffnm md_0_30 Outputs Md_0.30.xtc (Trajectory file) Md_0.30.gro Md_0.30.tpr

14. Data analsyis Things to note All plots generated from GROMACS (. xvg ) format can be plotted Using Q tGrace or XmGRACE

15. 1. Root-mean-square deviation (RMSD) Commands: gmx trjconv -s md_0_30.tpr -f md_0_30.xtc -o md_0_30_center.xtc -center - pbc mol - ur compact (Correcting the trajectory) gmx rms -s md_0_30.tpr -f md_0_30_center.xtc -o protein_rmsd.xvg -tu ns Outputs md_0_30_center.xtc (Corrected Trajectory) Protein_rmsd.xvg To evaluate stability of the protein by comparing structure of every frame with energy minimized initial structure

16. Molecular Dynamics Simulations - RMSD

17. 1. Radius of gyration ( Rg ) Commands: gmx gyrate -s md_0_30.tpr -f md_0_30_center.xtc -o gyrate.xvg Outputs gyrate.xvg To evaluate compactness of the structure

18. Molecular Dynamics Simulations – Radius of Gyration Average: 1.84nm

19. Rms Fluctuation ( rmsf ) Commands: gmx rmsf -s md_0_30.tpr -f md_0_30_center.xtc -o protein_rmsf.xvg – tu res To evaluate per residue flexibility Outputs Protein_rmsf.xvg

20. Molecular Dynamics Simulations – RMSF

21. Important links http:// www.mdtutorials.com/gmx/index.html (Detailed Tutorial) https://bioinformaticsreview.com/20151126/how-to-install-gromacs-5-x-x-on-linux-ubuntu-14-04-lts / (Installation Instructions)

22. Thank You By: Mayur Mukhi, WATER Lab., SSSIHL, PSN Campus