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MD Simulation

Tutorial: A quick MD simulation using NAMD and VMD

Dr. Muniba Faiza

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qwikmd

Molecular dynamics (MD) simulation has become an important methodology in research covering systems consisting of millions of atoms. We have provided several articles on MD simulation including the GROMACS [1] installation and performing MD. In this article, we will learn about “QwikMD” a plugin in NAMD [3], and VMD [4].

QwikMD allows users to set up the MD simulation of macromolecules in a few minutes. The steps are explained as follows.

  1. Open terminal (Ctrl+Alt+T) and type $ VMD. (If you are using Windows, then open a command prompt by typing ‘cmd’ in the search box and then type >VMD ).
  2. Go to Extensions --> Simulate --> QwikMD. A window will appear as shown in Fig. 1.

Fig. 1 A screenshot of QwikMD window launched from VMD

3. Now, load your protein structure either by typing or by browsing, then Click 'Load' .

It allows users to either simulate in an explicit solvent by simulating all atoms of the solvent or in an implicit solvent by adding a dielectric constant to the electrostatic calculation. For more information regarding this, click here. We are performing a simple MD and we will be using implicit solvent method.

4. Remove oxygen atoms from water molecules.

Click on 'Chain/Type Selection' and deselect the water molecules 'A and water'.

After that, you can see the oxygen atoms (red) in the VMD display will disappear.

5. Select the ‘Solvent’ and ‘Salt concentration’. Here, it is ‘implicit’ and default salt concentration (0.15 mol/L).

6. Now, move to the section ‘Simulation Set up’.

Check the 'Live View' checkbox for Live simulation and click 'Prepare'.

During this step, autopsf function is called to generate files required for MD simulation including NAMD configuration files. You will have to select a folder to save the input file named ‘.qwikmd‘.

After that, you will notice two folders will be created in the working directory: setup and run. All files created during the set up will be stored in the setup folder and those files that will be required for running MD simulation will be stored in run folder.

7. Move to another option “Protocol”.

Check the 'Equilibration' and 'MD' checkboxes and enter particular 'Temperature' and 'Simulation time'.

Here, the temperature was set to 27 C (300 K) and the simulation time was set to 1ns.

8. Run the simulation

Click 'Start MD Simulation'--> Select the number of CPU cores to be used to perform the simulation.

It might show an error (” Error connecting to localhost on port 3000“) until a connection is established between NAMD and VMD. The live simulation will be continued to run in the background until you abort it.

That’s it. Wait for the simulation to finish.

References

  1. Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX1, 19-25.
  2. Ribeiro, J. V., Bernardi, R. C., Rudack, T., Schulten, K., & Tajkhorshid, E. (2018). QwikMD-Gateway for Easy Simulation with VMD and NAMD. Biophysical Journal114(3), 673a-674a.
  3. Phillips, J. C., Zheng, G., Kumar, S., & Kalé, L. V. (2002, November). NAMD: Biomolecular simulation on thousands of processors. In SC’02: Proceedings of the 2002 ACM/IEEE conference on Supercomputing (pp. 36-36). IEEE.
  4. Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of molecular graphics14(1), 33-38.

 

 

 

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.

Dr. Muniba Faiza

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In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].

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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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