This document provides an overview of molecular dynamics simulations using GROMACS. It discusses the key components and steps involved, including preparing the protein, solvating the system, adding ions, energy minimization, and multiple equilibration steps. Data analysis techniques are also described, such as calculating the root mean square deviation (RMSD) to evaluate stability, radius of gyration to evaluate compactness, and root mean square fluctuation (RMSF) to evaluate per residue flexibility. The overall goal is to bring the molecule to a natural, dynamic state using computational modeling to mimic real-life physical forces.

1. MOLECULAR
DYNAMICS
SIMULATIONS
WITH
GROMACS
By:
Mayur 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 Inp
ut
Outpu
t
Outputs
Topology File (topol.top)
Position Restraint file
(posre.itp)
protein_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
Shape Siz
e
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

15. DATA ANALSYIS
THINGS TO NOTE
All plots generated from GROMACS (.xvg) format can be
plotted
Using QtGrace or XmGRACE

16. 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)
To evaluate stability of the protein by comparing
structure of every frame with energy minimized initial
structure

18. MOLECULAR
DYNAMICS
SIMULATION
S - RMSD

19. 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

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

21. 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

22. Molecular
Dynamics
Simulations –
RMSF

23. 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)

24. THANK YOU
By:
Mayur Mukhi,
WATER Lab.,
SSSIHL, PSN
Campus