This document provides an overview of molecular dynamics (MD) simulations and their analysis. MD simulations calculate the time-dependent behavior of molecules and can be used to study conformational changes in proteins and nucleic acids. The document outlines various analyses that can be done on MD simulations including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration, hydrogen bonding, secondary structure analysis using Ramachandran plots, free energy surfaces, and principal component analysis. It also provides examples of running MD simulations using VMD and applications of MD simulations such as understanding allostery and molecular docking.

1. Molecular Dynamics
Simulations

2. Overview
Introduction
Analysis of MD Simulation
➔Root mean square deviations and fluctuations (RMSD and RMSF)
➔ Radius of gyration
➔Hydrogen bonds
➔Secondary structure analysis
➔Free energy surfaces
➔Principal component analysis
Running MD Simulation using VMD
Applications
References

3. Introduction
MD Simulation
Developed in late 70s
Principal tool in study of biological molecules
Calculates time dependent behaviour of molecul
on fluctuations and conformational changes of proteins and nucleic acids
Follows the laws of classical mechanics, most notably Newton’s Law
Used to investigate structure, dynamics and thermodynamics o

4. MD Basic Algorithm
Abbreviations: Epot, potential energy;

5. Analysis of MD Simulation
1. Root mean square deviation (RMSD)
●Root mean square deviation (RMSD) is a measure of how structurally similar a protein is to a reference
where Natoms is the number of atoms whose positions are being compared and ri(t) is the position of atom
●High RMSDs tell us that a specific protein conformation is very different from a reference structure (in

6. Figure: RMSD plot in QwikMD

7. Analysis of MD Simulation
2. Root mean square fluctuation (RMSF)
●The root mean square fluctuation (RMSF) is a measure of the deviation between the position of particle
where T is the time over which one wants to average and ri
ref
is the reference position of particle i.
●Difference between RMSD and RMSF: The latter is averaged over time, giving a value for each particl

8. Figure: RMSF plot for a short CBH1 simulation

9. Analysis of MD Simulation
3. Radius of Gyration
To have a measure for the compactness of a structure, we can
calculate the radius of gyration:
where mi is the mass of atom i and ri is the position of atom i with respect to the center of mass of the

10. Analysis of MD Simulation
4. Hydrogen bonds
●To determine whether an H-bond exists between a donor D and an acceptor A, a geometrical criter

11. Figure: No. of Hydrogen bonds vs Time

12. Analysis of MD Simulation
5. Secondary Structure Analysis
●The DSSP (Dictionary of Secondary Structure for Proteins) program allows the analysis of secondary
●DSSP uses a pattern-recognition process of hydrogen-bonding and geometrical features:
− elementary H-bonding patterns: turn and bridge
− repeating turns = helices, repeating bridges = ladders
− connected ladders = sheets
− geometric structure defined in terms of torsion and curvature of differential geometry
− torsion → handedness of helices and twisted β-sheets
− curvature → curved pieces = bends
− solvent exposure = number of possible H2O molecules in contact with a residue

13. Analysis of MD Simulation
Secondary structure: Ramachandran Plot
A Ramachandran plot is the projection of the structure between two residues on the two dihedral ang

14. Beta sheet
Alpha helix
Left handed helix
Figure: Ramachandran plot in QwikMD

15. Analysis of MD Simulation
6. Free energy surfaces
●Biomolecular processes, such as folding or aggregation, can be described in terms of the molecule's f
where kB is the Boltzmann constant, P is the probability distribution of the molecular system along som
●Popular choices for R (so-called order parameters): Rg , rmsd, number of hydrogen bonds or native c
●Typically the free energy is plotted along two such order parameters, giving rise to a (reduced) free en

16. Analysis of MD Simulation
7. Principal component analysis
●Principal component analysis is also called covariance analysis or essential dynamics.
●It uses the covariance matrix σ of the atomic coordinates:
where q1,...,q3N are the mass-weighted Cartesian coordinates and ‹...› denotes the average over all
●Mathematically, it is a transformation of the data to a new coordinate system, in which the first co

17. Figure: PCA plot for a short CBH1 simulation performed in BIO3D

18. Running MD Simulation using VMD
1. Preparing a Molecular Dynamics Simulation
1.1 Finding the QwikMD Plugin
●Open VMD either using the desktop icon or by typing vmd in the terminal Window.
●To open QwikMD, click on Extensions → Simulation → QwikMD in the VMD Main window. You

21. 1.2 Loading an Initial Structure
●There are two ways to load a PDB file into QwikMD. If the file is already downloaded, click on th
●If not, enter the PDB code into the PDB ID bar and click Load. For this presentation, we will look
●After the molecule is loaded, it should show up in the OpenGL Display window as in the followin

23. 1.3 Preparing Input Files
●QwikMD allows users to prepare and run simulations using both explicit solvent, in which water mole
●Implicit solvent simulations are faster due to the smaller number of atoms, but they are less accurate th
●Here I will show the setup procedures for implicit solvent systems as I don’t have access to high-perfo
● To prepare an implicit solvent system, select Implicit in the solvent selection tab in the main QwikMD

24. Figure: Expanded QwikMD screen. Here, you can specify the temperature, simulation time, and simulation protocol.

25. 1.4 Preparing simulation files for a run
●Click Save under SimulationSetup in the main QwikMD window, enter a name for the system, a
●To begin the simulation, click Start Equilibration Simulation 0. This wil begin the equilibration
●After the equilibration run is finished, click Start Production Run 0 to begin the production MD
●After the run is finished, you should see these output files:
●1. A .dcd file. This is the trajectory file that contains the position of every atom at each saved sim
●2. Restart files (.restart.coor, .restart.vel, .restart.xsc). These contain the coordinates, velocity,
●3. A .log file. This will provide energy values at a specified time interval.

26. 1.5 Simple Analysis in QwikMD
●The following steps will show how to perform basic analysis of MD simulations within QwikMD.
1. Load a completed simulation run into QwikMD. Click Load under Simulation Setup in the main
2. Go to the Basic Analysis tab in the QwikMD window. Here, there are functions to compute root

27. Figure: RMSD plot in QwikMD which shows the RMSD during equilibration.

28. Applications
➢ Understanding allostery
➢Molecular docking and Drug design
➢Refining structure predictions

29. References
1. Berman HM, Battistuz T, Bhat TN, et al. The protein data bank. Acta Crystallogr D Biol Cryst. 200
2. Hospital A., Goni J.R., Orozco M., Gelpi J.L. Molecular dynamics simulations: Advances and appl
3. Ribeiro J., Bernardi R., Rudack T, et al. QwikMD — Integrative Molecular Dynamics Toolkit for N
4. Barnettster C., Senapathi T., Bray S. Analysis of molecular dynamics simulations (Galaxy Training