Gromacs/C2/Installation-of-VMD/English

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Visual Cue Narration
Slide Number 1

Title Slide

Welcome to the tutorial on Installation of VMD.
Slide Number 2

Learning Objectives

In this tutorial, we will learn to,
  • Download and install VMD 1.9.3 on
    • Ubuntu Linux 20.04 OS
    • Windows 10 OS
  • Open a pdb file
  • Change coloring and rendering
  • About sequence viewer
Slide Number 3

System and Software Requirement

To record this tutorial, I am using
  • Ubuntu Linux v20.04 OS
  • Firefox web browser v92
  • Windows 10 OS
  • Chrome web browser v89
  • VMD 1.9.3
  • A working internet connection
Slide Number 4

Pre-requisites

https://spoken-tutorial.org

To follow this tutorial,
  • Learner must be familiar with basic computer skills.
  • For pre-requisite tutorials, please visit this site.
Slide Number 5

Code Files

  • Files used in this tutorial are provided in the code files link.
  • Please download and extract the files.
  • Make a copy and then use them while practising.
Slide Number 6

Download Link for VMD

http://www.ks.uiuc.edu/Research/vmd/

  • The official website for VMD is shown here.
  • VMD is the acronym for Visual Molecular Dynamics.
Open web browser.

Go to, http://www.ks.uiuc.edu/Research/vmd/ .

Open a web browser and go to the VMD web page.
Place the cursor on the Software section on the top menu. Notice the Software section on the top menu.
Scroll down to VMD and select download from the submenu. Scroll down to VMD and select Download from the submenu.
Cursor on version 1.9.4 . The page refreshes.

Notice the current alpha version is 1.9.4.

We will install the 1.9.3 version which is more stable currently.

This number may likely be different for you when you practice this tutorial.

Downloadable options for various OS are seen here.

Click on LINUX_64 OpenGL, CUDA, OptiX, OSPRay . If using an older OS version, download an earlier version of the software.

Linux users, may click the link for the Linux version as seen here.

Click on Windows OpenGL, CUDA . Windows users click on the Windows 32 bit option.
Cursor on the registration link. The page refreshes to a registration or login page.

If this is the first time, please fill in a username and password at this time.

Click on Continue with .registration or download. Click on Continue with registration or download to proceed further.
Type a chosen user name and password. When using for first time, choose a user name and password for yourself.
Show details for filling in the form. In the refreshed page, fill in details in all the fields.

Learner need to give your name, email, affiliation and details as mentioned.

Click on Register. When done, click on Register.
Click on I agree to terms of this license. The page refreshes to the Terms of license page.

You may pause the video and read through the terms of agreement.

Click on I agree to the terms of this license.

Slide Number

Install VMD on Windows 10 OS

Let’s install VMD on Windows 10 OS.
Select the Save file option and click on Ok. The page refreshes and the file is downloaded to the computer.
Allow the file download to complete.
Open the File explorer and go to the Downloads folder. Open the File explorer and go to the Downloads folder.

Notice the downloaded file here.

Double click on vmd18451Win64-SetupV6.msi. Double click on the downloaded file to start the installation.
Click on Yes. Click on Yes on the user prompt that appears on the screen.
Click on Next. Click on Next, in the setup dialog box.
Click on Next. I will retain the default folder and path for installation.

Click on Next.

Click on Install. Let's click on Install.
Show the installation. Allow the installation to complete.
Click on Finish. Click on Finish to complete the installation.
Press the Windows key. To open VMD, press the windows key on the keyboard.
Type vmd in the search form.


Select vmd and double click.

In the search form type vmd and notice the installed vmd listed.

Click on it to open the program.

Show the three VMD windows that gets opened. VMD command prompt, a graphics display window and a menu window opens.
Slide Number

Install VMD on Ubuntu Linux OS

Now let’s download and install VMD on Ubuntu Linux OS.
Select the Save file option and click on Ok. The page refreshes and a save file dialog box opens.

Select the Save file option and click on Ok to start the download.

Allow the file download to complete.

Let’s install VMD using terminal commands.

Press Control+Alt+T keys together. Then open a terminal by pressing Control, Alt and T keys together.
Type Cd Downloads and press Enter. Change directory to the Downloads folder, since the file is downloaded here.
Type, tar -xvf vmd-1.9.3a51.bin.LINUXAMD64-CUDA102-OptiX650-OSPRay185.opengl.tar.gz and press Enter. Let’s unzip and extract the files from the tarball using the command as seen here.
Cursor on directory name vmd-1.9.3a51. A new directory gets created with the vmd the version number.

The files are extracted to this directory.

Press Ctrl+L. I will clear the screen for clarity in the video.
Type, cd vmd-1.9.3a51 and press Enter. Change path to this directory using the command as seen here.
Type, gedit README and press Enter. Open the README file in the text editor.

Go through the installation procedure.

Close the gedit widow. Pause this video, scroll down the file, and read the instructions as needed.

Let's close the text editor window.

Type ./configure and press Enter. Enter the command to ./configure and the press Enter key.
point to the output on the terminal. Notice the output of the command.
Type, cd src and press Enter. Now, change the directory to src using the command as seen here.
Press Ctrl+L. I will clear the screen for clarity in the video.
Type, sudo make install vmd and press Enter. Enter the install command as seen.

When prompted for the sudo password enter it to continue with installation.

Cursor on the path, /usr/local/bin/vmd. Allow the process to complete.

Notice the path of the installed VMD.

For me it is, usr local, bin, vmd.

Type, cd vmd and press Enter. Enter the command vmd, to open the VMD using the terminal.
Rearrange the three windows of VMD to see them clearly. First I will rearrange the three windows to see them conveniently.
Next, let’s select a pdb file to open in VMD.
Show screenshot of directory, /src/testuils/simulationdatabase/ in File Manager. Few test PDB files are provided along with Gromacs installation files.

They can be found in the testutils directory.

Navigate to the simulationdatabase directory.

Highlight lysozyme.pdb, in path, gromacs-2021.2\src\testutils\simulationdatabase . One of them is the PDB file, which is the truncated structure of lysozyme.
Copy lysozyme.pdb to Desktop folder. I will copy this file for now to the Desktop folder for ease of use.
Go to the VMD main window. Next, go to the VMD main window.
Click on File, New molecule. Click on File, New molecule to open a dialog box.
Click on Browse, which is seen against the File name. Click on Browse, which is seen against the File name.
choose the lysozyme.pdb file from Desktop. Choose a molecule file window opens.

I will choose the lysozyme.pdb file from Desktop.

Click on Ok. Click on Ok.
Click on the pull down for Determine File type. Click on the pull down for Determine File type.

Currently it is in PDB format.

Notice that VMD can open many file formats including Gromacs generated files.

Click on Load. Click on Load.
Close Molecule Fie Browser window. Let's close this window.
Show the molecule display. The coordinates of the atoms in the molecule gets loaded on the graphics window.
Show details in command prompt window. The command prompt window shows concise details of the molecule.
Show to rotate the molecule. To rotate a molecule, left click, hold and move the mouse in any direction.
Arrow on the axis on left bottom corner. Notice the axis information on the left bottom side.
Click on on Display and uncheck the depth cue box. Currently, the molecule is displayed with depth cue.

To change this, click on Display and uncheck the box for Depth cue.

Press the S key on the keyboard. To, change zoom level, press the S key on the keyboard.

Notice a two direction arrow in the graphics window.

Use the mouse scroll wheel to adjust zoom level. Use the mouse scroll wheel to adjust to desired zoom level.
Click on Mouse on the top menu. Click on Mouse on the top menu in the Main window.

Notice the options and shortcut keys for rotate, translate and scaling.

Press the R key on the keyboard. Press the R key on the keyboard to change the mode to rotate.
Click on Display, Representations. Let’s change the display mode next.

Choose, Display, Representations.

Cursor on Selected molecule. On the top, notice the molecule name for Selected molecule.

There is only one molecule loaded now.

So the pulldown has only one molecule listed.

Cursor on Selected atoms. All atoms in the molecule are selected now.
For Drawing Methods, select Ribbons

Add annotation "Some users may need to click on Apply to notice the changes".

For Drawing Methods, select Ribbons.

Notice the ribbon model in the graphics window.

For Coloring method, choose Element. Next, for Coloring method, choose Element.
Choose Bonds for Drawing Methods.

Add annotation "Some users may need to click on Apply to notice the changes".

I will also choose Bonds for Drawing Methods .
Show changed view in graphics window. Again notice the changes in the graphics window.
Close Graphical Representations window. Let's close this window.
Go to Extensions, Analysis and choose Sequence viewer. Now go to Extensions, Analysis and choose Sequence viewer.
Cursor at the secondary structure on the right and at the bottom. A new Sequence Viewer Window opens.

Notice the secondary structure displayed on the right and at the bottom.

Click on any residue and notice the residue highlighted in the graphics window. Click on any residue and notice the residue highlighted in the graphics window.

Learner must practice and familiarise with VMD further.

Click on File, Quit.

In the Really quit VMD prompt, choose Yes.

To quit VMD, choose, File, Quit.

If a prompt reading Really quit appears, choose Yes.

Slide Number 7

Summary

Now let’s summarize. In this tutorial, we
  • Downloaded and installed VMD 1.9.3 on
    • Ubuntu Linux 20.04 OS
    • Windows 10 OS
  • Loaded a PDB file
  • Changed rendering and coloring
  • About Sequence viewer
Slide Number 8

Assignment

For assignment activity, please do the following.
  • Open 1AKI.pdb file in VMD.
  • Explore coloring methods, CPK and VDW representations.
  • Explore Sequence viewer window and secondary structure details of the protein.
Slide Number 9

Spoken Tutorial Project

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Slide Number 10

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Slide Number 11

Forum for questions

Please post your timed queries in this forum.
Slide Number 12

Acknowledgement

Spoken Tutorial Project is funded by MoE, Government of India.
This is Rani from IIT, Bombay. Thank you for joining.

Contributors and Content Editors

Ranipv076, Snehalathak

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