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MD Simulation

Tutorial: MD simulation output analysis of protein using GROMACS

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Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of insulin (PDB ID: 1ZNI) was performed using GROMACS. The output analysis of that simulation is explained in this article.

The last MD simulation of insulin protein was performed at 1 ns. The same output files will be used to analyze the results.

The trjconv module will be used for trajectory analysis. But before starting the analysis, we need to correct the trajectory because it might be possible that the protein may appear broken or located on any side of the box other than being in the center. To do this, we need .tpr and .xtc files as input that we obtained from the final MD run. Open the terminal, and type the following command:

$ gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -center

When prompted, type “1” for selecting “Protein” as the group to be centered and “0” for “System”. It will generate md_0_1_noPBC.xtc as output that will be used for the analysis as shown below.

 1. RMSD

Root mean square deviation (RMSD) calculates the deviation between the two structures. gmx rms module is used to calculate the RMSD of the simulated protein.

$ gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -o rmsd.xvg -tu ns

here, -tu refers to time units.

When prompted, type “4” for selecting “Backbone” and “0” for “System”. It will generate rmsd.xvg file that can be plotted using xmgrace software. The RMSD plot for this simulation looks like this:

Fig. 1 RMSD plot of insulin simulated at 1ns.

RMSD relative to the crystal structure present in the minimized equilibrated system can also be calculated using the following command:

$ gmx rms -s em.tpr -f md_0_1_noPBC.xtc -o rmsd_cyrstal.xvg -tu ns

The plot is shown in Fig. 2.

 

Fig. 2 RMSD plot relative to the minimized and equilibrated crystal structure of insulin.

2. RMSF

Root Mean Square Fluctuation (RMSF) calculates the fluctuation of atoms at positions in the trajectory. gmx rmsf module will be used to calculate the RMSF of the simulated protein.

$ gmx rmsf -f md_0_1_noPBC.xtc -s md_0_1.tpr -o rmsf.xvg

When prompted, type “1” for “Protein”. The generated plot is shown in Fig. 3.

Fig. 3 RMSF plot of simulated insulin protein.

If you want to see RMSF wrt residues then use the following command:

$ gmx rmsf -f md_0_1_noPBC.xtc -s md_0_1.tpr -o rmsf.xvg -res

3. Radius of gyration

The radius of gyration calculates the radii of gyration of a molecule about the three axes (x, y, and z) as a function of time. gmx gyrate module is used for this.

$ gmx gyrate -f md_0_1_noPBC.xtc -s md_0_1.tpr -o gyrate.xvg

When prompted, type “1” for protein. The generated plot is shown in Fig. 4.

Fig. 4 Radius of gyration plotted for insulin simulated at 1ns.

4. Hydrogen bonds

gmx hbond module is used to analyze hydrogen bonds that are calculated on the basis of cutoffs for the angle Hydrogen – Donor-Acceptor and the distance Donor-Acceptor (or Hydrogen – Acceptor). Generally, quite useful in complex analysis.

$ gmx hbond -f md_0_1_noPBC.xtc -s md_0_1.tpr -num -dist

here, -num calculates the number of hydrogen bonds and -dist calculates the average distance among them.

When prompted, type “1” for “Protein” and select the other group that does not overlap with the protein, for example, here in this simulation, we have selected “11” for “Non-protein”. If you are performing a complex simulation, then you can select Protein and Ligand. This will display the status of hydrogen bonds between the protein and the ligand. In that case, it is helpful in analyzing the stability of hydrogen bonds between the receptor and ligand. The generated plots are shown in Fig. 5 & 6.

Fig. 5 Number of hydrogen bonds calculated between the protein and non-protein.

Fig. 6 Distribution of hydrogen bonds calculated between the protein and non-protein.

These are the basic modules that are used to analyze MD simulations. You can always use additional arguments in these modules and the other modules as well.

MD simulation of a receptor-ligand complex will be explained in the upcoming articles.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

MD Simulation

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing VIAMD on Ubuntu (Linux).

Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).

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MD Simulation

Energy minimization and equilibration of simple protein using NAMD & VMD.

Dr. Muniba Faiza

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Energy minimization and equilibration of simple protein using NAMD & VMD.

In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.

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MD Simulation

Generating topology of molecule for AMBER forcefield for GROMACS.

Dr. Muniba Faiza

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Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.

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MD Simulation

How to visualize output plots of MD simulation (GROMACS)?

Dr. Muniba Faiza

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How to visualize output plots of MD simulation (GROMACS)?

Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)

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MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

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How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.

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MD Simulation

How to calculate number of steps (nsteps) for MD simulation run?

Dr. Muniba Faiza

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How to calculate number of steps (nsteps) for MD simulation run?

While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)

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MD Simulation

How to install GROMACS on Apple M1 (MacOS)?

Dr. Muniba Faiza

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Installing GROMACS on Apple M1 (MacOS)

We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)

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MD Simulation

How to take snapshots of structure at specific times in GROMACS?

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How to take snapshots of structure at specific times in GROMACS?

It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)

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MD Simulation

GROMACS: Uses & Applications

Dr. Muniba Faiza

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GROMACS: Uses & Applications

GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)

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MD Simulation

Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Dr. Muniba Faiza

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Installing GROMACS on ubuntu

We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)

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MD Simulation

How to create an index file in GROMACS for MD simulation?

Dr. Muniba Faiza

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How to create an index file in GROMACS for MD simulation?

MD simulation is a tricky technique if you don’t understand what you are doing through various parameters and algorithms in GROMACS [1]. That may lead to several errors. In this article, we are going to create an index file for the protein groups in GROMACS to solve such errors. (more…)

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MD Simulation

How to generate topology of small molecules & ligands for MD Simulation?

Dr. Muniba Faiza

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generate topology of small molecules & ligands for MD simulation

Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)

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MD Simulation

Tutorial: MD Simulation of small organic molecules using GROMACS

Dr. Muniba Faiza

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MD Simulation of small molecules

GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of small organic molecules. (more…)

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MD Simulation

Tutorial: MD simulation with mixed solvents using GROMACS

Dr. Muniba Faiza

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MD simulation with mixed solvents

In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD simulation of a simple protein and a protein-ligand complex. (more…)

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MD Simulation

Tutorial: MD simulation output analysis of a complex using GROMACS

Dr. Muniba Faiza

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MD simulation output analysis of a complex using GROMACS

We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex. (more…)

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MD Simulation

How to submit MD simulation job on a cluster server using PBS script?

Dr. Muniba Faiza

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MD Simulation on cluster server

Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)

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MD Simulation

Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support

Dr. Muniba Faiza

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Install gromacs with gpu acceleration

GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration. (more…)

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MD Simulation

Installing GROMOS96 on Ubuntu

Dr. Muniba Faiza

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Installing gromos96 on Ubuntu

GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu. (more…)

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MD Simulation

MD Simulation using GROMACS: Things to remember

Dr. Muniba Faiza

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MD Simulation

Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)

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MD Simulation

Video Tutorial: MD Simulation using GROMACS

Dr. Muniba Faiza

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Video Tutorial: MD simulation using GROMACS

This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.

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