View source for Gromacs/C2/Installation-of-VMD/English




{| border=1
|  | '''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/ 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/ 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/ 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 [https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1515 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 [https://www.ks.uiuc.edu/Development/Download/download.cgi?UserID=&AccessCode=&ArchiveID=1484 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 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'''

'''Summary 11'''
|  | 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'''

'''Assignment 13'''
|  | 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 14'''

'''Spoken Tutorial Project'''
|  | This video summarises the Spoken Tutorial Project.

Please download and watch it.

|-
|  | '''Slide Number 15'''

'''Spoken Tutorial workshops'''
|  | We conduct workshops using spoken tutorials and give certificates. 
Please write to us.

|-
|  | '''Slide Number 16'''
'''Forum for questions'''
|  | Please post your timed queries in this forum.

|-
|  | '''Slide Number 18'''

'''Acknowledgement'''
|  | Spoken Tutorial Project is funded by MoE, Government of India.

|-
|  | 
|  | This is Rani from IIT, Bombay. Thank you for joining.

|-
|}