View source for Gromacs/C2/Installation-of-Gromacs-on-Windows-OS/English

{| border=1
|  | '''Visual Cue'''
|  | '''Narration'''

|-
|  | '''Slide Number 1'''

'''Title Slide '''
|  | Welcome to the tutorial on '''Installation of Gromacs on WIndows 10 OS'''.

|-
|  | '''Slide Number 2'''

'''Learning Objectives'''
|  | In this tutorial, we will learn to,
* Install '''Ubuntu''' 20.04 '''LTS''' app on '''Windows''' 10 OS 
* Install programs essential to build '''Gromacs'''
* Download and build '''gromacs''' 2021.2

|-
|  | '''Slide Number 3'''

'''Learning Objectives'''
|  | * Test the installation with the '''help''' command
* About alternate installation method with the '''sudo apt-get''' command.

Installation may take a few hours depending on the hardware.

|-
|  | '''Slide Number 4'''

'''System and Software Requirement'''
|  | To record this tutorial, I am using

* '''Windows''' 10 OS
* '''Google Chrome '''v92
* '''Ubuntu''' 20.04 '''LTS''' app
* '''Gromacs''' v2021.2
* A working internet connection

|-
|  | '''Slide Number 5'''

'''System and Software Requirement'''
|  | * 64-bit architecture and 4GB RAM or higher are must for the installation
* All the '''Windows''' OS updates completed
* Sufficient disk space must be available for software build

|-
|  | '''Slide Number6'''

'''Pre-requisites'''
|  | To follow this tutorial, * Learner must be familiar with basic computer skills.

|-
|  | '''Slide Number 7'''

'''Download Link'''
[http://www.gromacs.org/ http://www.gromacs.org/ ]
|  | The official website of '''Gromacs''' is shown here.

The software is available for '''Linux''' and '''Windows''' OS.
|-
|  | Open web browser and go to 

[http://www.gromacs.org/ http://www.gromacs.org] .
|  |Open a web browser and go to the '''Gromacs''' website.

|-
|  | Click on the '''Downloads''' section in the left panel.
|  | Click on the '''Downloads''' section in the left panel.

|-
|  | Hover mouse over '''downloaded here''' in the right panel and click on it.
|  | The web page is being redesigned at this time.

Click on the '''downloaded here'''.

|-
|  | Hover mouse over '''Current Release Candidate'''. 

Click on the Download link below.
|  | Click on the '''Download''' link seen below.

|-
|  | Cursor next to '''Current Release Candidate'''.
|  | When you practise this tutorial, the version number may be different.

|-
|  | Hover mouse over '''ftp''' and '''http''' download options.
|  | A new page may open with a welcome message for some users.

Under the '''Source code''' section, notice the '''ftp''' and '''https''' options.

I will note down the '''ftp''' address for later use.

|-
|  | Press the '''Windows''' key.
|  | Let’s first set up a '''Linux''' environment in '''Windows'''.

Press the '''Windows''' key on the keyboard.

|-
|  | In the search form, type '''control panel''' and press '''Enter'''.
|  | In the search form, type '''control panel''' and press '''Enter'''.

|-
|  |Scroll down the'''Control panel''' and click on '''Programs and Features'''.
|  |Scroll down the'''Control panel''' and click on '''Programs and Features'''.

For some of you it will be called '''Programs'''.

A '''Programs and Features''' window opens.

|- 
||In the left panel, click on '''Turn Windows Features on or off'''.
||In the left panel, click on '''Turn Windows Features on or off'''.

|-
|  |Scroll down and check the box for '''Windows subsystem for Linux'''.

Click on '''Ok'''.
|  |The '''Windows Features''' dialog box opens.

Scroll down and check the box for'''Windows Subsystem for Linux'''.

Click on '''Ok'''.

|-
|  |Click on '''Restart Windows'''.
|  | The system gathers the required information.

A prompt appears asking the user to'''Restart Windows'''.

Click on '''Restart Windows''', to complete the updates.

|-
|  |Type '''Microsoft store''' in the search form and press'''Enter'''.
|  |After '''Windows''' has restarts, open the'''Microsoft store'''.

|-
|  |Type '''microsoft store''' in the search form.
|  |Type '''microsoft store''' in the search form.

The '''microsoft store''' window opens. 

|-
|  |Type '''ubuntu 20.04 LTS''' in the search form.
|  |Type '''ubuntu 20.04 LTS''' in the search form.

The desired app is the first search result for me.

|-
|  |Click on'''ubuntu 20.04 LTS''' icon.
|  | Click on it to see the details.

|-
|  |Scroll down and click on blue coloured '''Get button.'''

If prompted, click on '''No, Thanks'''.
|  |Scroll down and click on '''Get''' to install the '''Ubuntu''' 20.04'''LTS''' app.


If prompted, click on '''No, Thanks'''.
|-
|  |Close the '''Microsoft store'''.
|  | Allow the process to be completed.


After the app is installed,close the '''Microsoft store'''.
|-
|  |Press the '''Windows''' key, type '''Ubuntu''' 20.04'''LTS'''.
|  |Press the '''Windows''' key, type '''Ubuntu''' 20.04'''LTS''' and notice the'''Ubuntu''' app.

|-
|  |Open '''Ubuntu''' 20.04'''LTS'''.
|  | Click on it to open it. 

Notice the initializing message.

|-
|  | 
|  | It will take some time to complete the process.

|-
|  |Type a user name of choice and press '''Enter'''.
|  | The very first time, user is prompted to enter a new user name. 

I will type my name and press '''Enter'''.

You may enter your name.

|-
|  | Cursor on password prompt.
|  | Next, the prompt asks for a password.

|-
|  | Enter a password of your choice and reconfirm it.
|  | Enter your choice of password and reconfirm it in the next step.

|-
|  | Press '''Ctrl+L'''.
|  | Now the user account setup is complete.

I will clear the screen for clarity.

|-
|  | Show Properties option in terminal.
|  | I will increase the font size for clarity, using the properties option.

You may also do so, if desired.

|-
|  |Type, '''sudo apt-get update''' and press '''Enter'''.
|  |In the '''terminal''' enter the command as seen to update the library links. 

Allow the process to complete.

|-
|  |Press '''Ctrl+L'''.
|  | I will clear the screen for clarity.

|-
|  |Type, '''sudo apt-get upgrade '''and press '''Enter'''.
|  |In the '''terminal''' enter the command as seen to update the library links. 

|-
|  | Enter the '''sudo password'''.
|  | Enter the '''sudo password''' if prompted.

Allow the process to complete.

|-
|  |Press '''Ctrl+L'''.
|  | I will clear the screen for clarity.

|-
|  |Type, '''sudo apt-get upgrade '''and press '''Enter'''.
|  |In the '''terminal''' enter the command as seen to upgrade the library links. 

Again, allow the process to complete.

|-
|  |Press '''Ctrl+L'''.
|  | Again, I will clear the screen for clarity in the video.

|-
|  |Type, '''sudo apt-get install -y build-essential make cmake gcc''' and press '''Enter'''.

Enter the sudo password if prompted.
|  | Next, issue the command as seen here.


This will install the programs and libraries essential for subsequent steps.

Enter the sudo user password if prompted. 

|-
|  | 
|  | Allow the process to be completed.

These processes take time. 

Make sure to watch the messages for any errors.

|-
|  |Press '''Ctrl+L'''.
|  | Again, I will clear the screen for clarity.

|-
|  |Type, '''mkdir gromacs''' and press '''Enter'''.
|  |Next, create a directory named '''gromacs''' using the command seen here.

|-
|  |Type, '''cd gromacs''' and press '''Enter'''.
|  | Let’s change to the newly created directory.

|-
|  |Type, '''wget[https://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz  ][https://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz https://ftp.gromacs.org/gromacs/gromacs-2021.2.tar.gz] and press '''Enter'''.
|  | Enter the command as seen, to download the '''gromacs'''    tarball for installation.

|-
|  |Type,'''tar -xvf gromacs-2021.2.tar.gz '''and press '''Enter'''.
|  | Extract the files from '''tarball''' with the command as seen here.

|-
|  | 
|  | The files get extracted to a new directory as seen here.

|-
|  |Press '''Ctrl+L'''.
|  | I will again clear the screen for clarity.

|-
|  |Type,'''cd gromacs-2021.2 '''and press '''Enter'''.
|  | The files get extracted to a new directory as seen here.

Let’s change the path to the newly created directory as seen here.

|-
|  |Show the '''gromacs-2012.2''' folder in the '''file  manager'''.
|  |For me this particular path is in the'''Downloads''' folder in'''Windows'''.

|-
|  | 
|  | For you it may be different.

|-
|  |Type,'''vim INSTALL ''' and press '''Enter'''.
|  |Type'''vim space INSTALL '''to open the file in '''vim'''  text editor.

|-
|  | Show installation instructions.
|  | Scroll down the file using page down or down arrow key. 

Detailed stepwise commands to install'''Gromacs''' is given here.

|-
|  | Type, ''':q!''' and press '''Enter'''.
|  | To quit the text editor, first type '''colon''' followed by '''q!''' and press '''Enter'''.

The command is visible at the bottom left of the screen. 

|-
|  | Type, '''mkdir build''' and press '''Enter'''.
|  | Next, create a new directory called '''build''' with the '''mkdir''' command.

|-
|  | Type, '''cd build''' and press '''Enter'''.
|  | Change the path to the newly created '''build '''directory as seen here.

|-
|  | Type '''sudo cmake .. -DGMX_BUILD_OWN_FFTW=ON '''and press '''Enter'''.
|  |To start'''Gromacs build''', enter the command as seen here.

|-
|  | Press '''Ctrl+L'''.
|  | Allow the process to be completed.

I will clear the screen for clarity in the video.

|-
|  | Type '''sudo make''' and press the '''Enter'''.
|  | Next, type '''sudo space make''' and press the '''Enter''' key.

|-
|  | Show the build process on the screen,
|  | All these processes take time.

Please be patient and allow them to complete. 

Watch for any error messages.

|-
|  |Press'''Ctrl+L'''.
|  | Again, I will clear the screen for clarity in the video.

|-
|  | Type '''sudo make install''' and press the '''Enter'''.
|  | Enter the command, '''sudo make install''' and press the '''Enter''' key.

|-
|  | Press '''Ctrl+L'''.
|  | With this step the installation process for '''gromacs''' is completed.

I will clear the screen for clarity in the video.

|-
|  |Type '''ls''' and press the '''Enter'''. key.
|  |Now enter the command '''ls''' to list the files in the '''build''' directory.

|-
|  |Show the files in the '''build''' directory.
|  | Notice the several files and directories created here.


These files were created during the build process of '''Gromacs'''.

|-
|  |Type '''cd bin''' and press '''Enter'''.
|  |Change to the bin directory with'''cd space bin''' command.

|-
|  |Type'''ls''' and press the'''Enter'''.
|  | List the files and notice the '''gmx''' executable here.

|-
|  |Type'''cd''' and press the '''Enter''' key.
|  | Enter the command '''cd ''' to go to the '''home''' directory.

|-
|  | Type '''whereis gromacs''' and press ‘’’Enter’’’. 
to check if files are in /usr/local/gromcs/ directory.
|  | Gromacs may get installed in'''usr local gromacs''' directory.

Check if it is in this directory for you.

Please list the files and using the command as seen here.

|-
|  | 
|  | Note down the path of installation.

|-
|  |Type '''vim .bashrc''' and press the'''Enter'''.
|  | Let’s edit the '''dot bashrc''' file with the command seen here.

|-
|  | Scroll to the bottom of the file.
|  | Scroll down to the bottom of the file with the page down or by using the down arrow key.

|-
|  | Press the '''Insert''' key.
|  | Go to edit mode by pressing the '''Insert''' key on the keyboard.

|-
|  |Use the arrow key and press '''Enter''' to start a new line.

Type,'''alias gmx='/usr/local/gromacs/bin/gmx'''' 
|  | Start a new line at the end and type the alias for '''gmx''' as seen here.

Use the path where '''Gromacs''' is installed in your computer. 

|-
|  | 
|  | Learners must enter the path of the gmx file. 

|-
|  | Press the '''Esc''' key.
|  | Press the '''Escape''' key to exit the edit mode in '''vim'''.

|-
|  |Type ''':wq''' and press '''Enter'''.
|  | To save and exit, type '''colon w q''' without '''whitespace''' and press '''Enter'''.

|-
|  |Type'''source .bashrc''' and press'''Enter'''.
|  | Let’s '''source''' to the updated '''.bashrc''' file as seen here.

|-
|  |Type '''gmx help grompp''' and press Enter.
|  | Next, test the installation with the '''gmx help grompp''' command as seen.

|-
|  | 
|  | I don’t see any errors in the output. 

This shows, we have installed '''Gromacs'''.

|-
|  | '''Slide Number 8'''

'''Alternate installation method'''
|  | For alternate installation method, do the following. 

* Issue the following commands in the '''terminal''' after '''Ubuntu app''' installation.
* Enter the command, '''sudo apt-get update'''

|-
|  | '''Slide Number 9'''

'''Alternate installation method'''
|  | * Enter the user '''sudo''' password if prompted
* Enter the command, '''sudo apt-get upgrade'''
* Then, enter the command, '''sudo apt-get install gromacs'''

|-
|  | '''Slide Number 10'''

'''Software Version'''
|  | * The latest version of the software may not get installed with this method
* The version with the '''linux''' repository will get installed

|-
|  | '''Slide Number 11'''

'''Summary'''
|  | Now let’s summarize. In this tutorial, we
* Installed '''Ubuntu 20.04 LTS''' app
* Installed essential programs to build '''Gromacs'''
* Downloaded and built '''Gromacs'''
* Tested the installation
* About alternate installation method

|-
|  | '''Slide Number 12''

'''Assignment'''

[https://www.gromacs.org/ https://www.gromacs.org/]
|  | For assignment activity, please do the following. 

* Go to the '''Gromacs '''website as seen here
* Go through the user support and documentation
* Read research papers of your choice which use '''Gromacs'''

|-
|  | '''Slide Number13'''

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

Please download and watch it.

|-
|  | '''Slide Number14'''

'''Spoken Tutorial workshops'''
|  | We conduct workshops using spoken tutorials and give certificates. 

Please write to us.

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

'''Forum for questions'''
|  | * Please post your timed queries in this forum.

|-
|  | '''Slide Number 16'''

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

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

|}