Difference between revisions of "Gromacs/C2/Installation-of-Gromacs-on-Windows-OS/English"

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Line 118: Line 118:
  
 
|-
 
|-
−
|  |Scroll down and check the box for'''Windows subsystem for Linux'''.
+
|  |Scroll down and check the box for '''Windows subsystem for Linux'''.
  
 
Click on '''Ok'''.
 
Click on '''Ok'''.
−
|  |The'''Windows Features''' dialog box opens.
+
|  |The '''Windows Features''' dialog box opens.
  
 
Scroll down and check the box for'''Windows Subsystem for Linux'''.
 
Scroll down and check the box for'''Windows Subsystem for Linux'''.
Line 128: Line 128:
  
 
|-
 
|-
−
|  |Click on'''Restart Windows'''.
+
|  |Click on '''Restart Windows'''.
 
|  | The system gathers the required information.
 
|  | The system gathers the required information.
  
 
A prompt appears asking the user to'''Restart Windows'''.
 
A prompt appears asking the user to'''Restart Windows'''.
  
−
Click on'''Restart Windows''', to complete the updates.
+
Click on '''Restart Windows''', to complete the updates.
  
 
|-
 
|-
−
|  |Type'''Microsoft store''' in the search form and press'''Enter'''.
+
|  |Type '''Microsoft store''' in the search form and press'''Enter'''.
−
|  |After'''Windows''' has restarts, open the'''Microsoft store'''.
+
|  |After '''Windows''' has restarts, open the'''Microsoft store'''.
  
 
|-
 
|-
−
|  |Type'''microsoft store''' in the search form.
+
|  |Type '''microsoft store''' in the search form.
−
|  |Type'''microsoft store''' in the search form.
+
|  |Type '''microsoft store''' in the search form.
  
 
The '''microsoft store''' window opens.  
 
The '''microsoft store''' window opens.  
  
 
|-
 
|-
−
|  |Type'''ubuntu 20.04 LTS''' in the search form.
+
|  |Type '''ubuntu 20.04 LTS''' in the search form.
−
|  |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.
 
The desired app is the first search result for me.
Line 156: Line 156:
  
 
|-
 
|-
−
|  |Scroll down and click on blue coloured'''Get button.'''
+
|  |Scroll down and click on blue coloured '''Get button.'''
  
−
If prompted, click on'''No, Thanks'''.
+
If prompted, click on '''No, Thanks'''.
−
|  |Scroll down and click on'''Get''' to install the'''Ubuntu''' 20.04'''LTS''' app.
+
|  |Scroll down and click on '''Get''' to install the '''Ubuntu''' 20.04'''LTS''' app.
  
  
−
If prompted, click on'''No, Thanks'''.
+
If prompted, click on '''No, Thanks'''.
 
|-
 
|-
−
|  |Close the'''Microsoft store'''.
+
|  |Close the '''Microsoft store'''.
 
|  | Allow the process to be completed.
 
|  | Allow the process to be completed.
  
  
−
After the app is installed,close the'''Microsoft store'''.
+
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'''.
−
|  |Press the'''Windows''' key, type'''Ubuntu''' 20.04'''LTS''' and notice the'''Ubuntu''' app.
+
|  |Press the '''Windows''' key, type '''Ubuntu''' 20.04'''LTS''' and notice the'''Ubuntu''' app.
  
 
|-
 
|-
−
|  |Open'''Ubuntu''' 20.04'''LTS'''.
+
|  |Open '''Ubuntu''' 20.04'''LTS'''.
 
|  | Click on it to open it.  
 
|  | Click on it to open it.  
  
Line 184: Line 184:
  
 
|-
 
|-
−
|  |Type a user name of choice and press'''Enter'''.
+
|  |Type a user name of choice and press '''Enter'''.
 
|  | The very first time, user is prompted to enter a new user name.  
 
|  | The very first time, user is prompted to enter a new user name.  
  
−
I will type my name and press'''Enter'''.
+
I will type my name and press '''Enter'''.
  
 
You may enter your name.
 
You may enter your name.
Line 212: Line 212:
  
 
|-
 
|-
−
|  |Type,'''sudo apt-get update''' and press'''Enter'''.
+
|  |Type, '''sudo apt-get update''' and press '''Enter'''.
−
|  |In the'''terminal''' enter the command as seen to update the library links.  
+
|  |In the '''terminal''' enter the command as seen to update the library links.  
  
 
Allow the process to complete.
 
Allow the process to complete.
  
 
|-
 
|-
−
|  |Press'''Ctrl+L'''.
+
|  |Press '''Ctrl+L'''.
 
|  | I will clear the screen for clarity.
 
|  | I will clear the screen for clarity.
  
 
|-
 
|-
−
|  |Type,'''sudo apt-get upgrade '''and press'''Enter'''.
+
|  |Type, '''sudo apt-get upgrade '''and press '''Enter'''.
−
|  |In the'''terminal''' enter the command as seen toupdate the library links.  
+
|  |In the '''terminal''' enter the command as seen to update the library links.  
  
 
|-
 
|-
Line 232: Line 232:
  
 
|-
 
|-
−
|  |Press'''Ctrl+L'''.
+
|  |Press '''Ctrl+L'''.
 
|  | I will clear the screen for clarity.
 
|  | I will clear the screen for clarity.
  
 
|-
 
|-
−
|  |Type,'''sudo apt-get upgrade '''and press'''Enter'''.
+
|  |Type, '''sudo apt-get upgrade '''and press '''Enter'''.
−
|  |In the'''terminal''' enter the command as seen to upgrade the library links.  
+
|  |In the '''terminal''' enter the command as seen to upgrade the library links.  
  
 
Again, allow the process to complete.
 
Again, allow the process to complete.
  
 
|-
 
|-
−
|  |Press'''Ctrl+L'''.
+
|  |Press '''Ctrl+L'''.
 
|  | Again, I will clear the screen for clarity in the video.
 
|  | 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'''.
+
|  |Type, '''sudo apt-get install -y build-essential make cmake gcc''' and press '''Enter'''.
  
 
Enter the sudo password if prompted.
 
Enter the sudo password if prompted.
Line 265: Line 265:
  
 
|-
 
|-
−
|  |Press'''Ctrl+L'''.
+
|  |Press '''Ctrl+L'''.
 
|  | Again, I will clear the screen for clarity.
 
|  | Again, I will clear the screen for clarity.
  
 
|-
 
|-
−
|  |Type,'''mkdir gromacs''' and press'''Enter'''.
+
|  |Type, '''mkdir gromacs''' and press '''Enter'''.
−
|  |Next, create a directory named'''gromacs''' using the command seen here.
+
|  |Next, create a directory named '''gromacs''' using the command seen here.
  
 
|-
 
|-
−
|  |Type,'''cd gromacs''' and press'''Enter'''.
+
|  |Type, '''cd gromacs''' and press '''Enter'''.
 
|  | Let’s change to the newly created directory.
 
|  | 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'''.
+
|  |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.
+
|  | Enter the command as seen, to download the '''gromacs'''   tarball for installation.
  
 
|-
 
|-
−
|  |Type,'''tar -xvf gromacs-2021.2.tar.gz '''and press'''Enter'''.
+
|  |Type,'''tar -xvf gromacs-2021.2.tar.gz '''and press '''Enter'''.
 
|  | Extract the files from '''tarball''' with the command as seen here.
 
|  | Extract the files from '''tarball''' with the command as seen here.
  
Line 289: Line 289:
  
 
|-
 
|-
−
|  |Press'''Ctrl+L'''.
+
|  |Press '''Ctrl+L'''.
 
|  | I will again clear the screen for clarity.
 
|  | I will again clear the screen for clarity.
  
 
|-
 
|-
−
|  |Type,'''cd gromacs-2021.2 '''and press'''Enter'''.
+
|  |Type,'''cd gromacs-2021.2 '''and press '''Enter'''.
 
|  | The files get extracted to a new directory as seen here.
 
|  | The files get extracted to a new directory as seen here.
  
Line 299: Line 299:
  
 
|-
 
|-
−
|  |Show the'''gromacs-2012.2''' folder in the file''' manager'''.
+
|  |Show the '''gromacs-2012.2''' folder in the '''file  manager'''.
 
|  |For me this particular path is in the'''Downloads''' folder in'''Windows'''.
 
|  |For me this particular path is in the'''Downloads''' folder in'''Windows'''.
  
Line 307: Line 307:
  
 
|-
 
|-
−
|  |Type,'''vim INSTALL '''and press'''Enter'''.
+
|  |Type,'''vim INSTALL ''' and press '''Enter'''.
−
|  |Type'''vimspaceINSTALL '''to open the file in'''vim''' text editor.
+
|  |Type'''vim space INSTALL '''to open the file in '''vim''' text editor.
  
 
|-
 
|-
Line 367: Line 367:
  
 
|-
 
|-
−
|  |Type'''ls''' and press the'''Enter'''.
+
|  |Type '''ls''' and press the '''Enter'''. key.
−
|  |Now enter the command'''ls''' to list the files in the'''build''' directory.
+
|  |Now enter the command '''ls''' to list the files in the '''build''' directory.
  
 
|-
 
|-
−
|  |Show the filesin the'''build''' directory.
+
|  |Show the files in the '''build''' directory.
 
|  | Notice the several files and directories created here.
 
|  | Notice the several files and directories created here.
  
Line 378: Line 378:
  
 
|-
 
|-
−
|  |Type'''cd bin''' and press'''Enter'''.
+
|  |Type '''cd bin''' and press '''Enter'''.
 
|  |Change to the bin directory with'''cd space bin''' command.
 
|  |Change to the bin directory with'''cd space bin''' command.
  
Line 386: Line 386:
  
 
|-
 
|-
−
|  |Type'''cd ~''' and press the'''Enter'''.
+
|  |Type'''cd''' and press the '''Enter''' key.
−
|  | Enter the command '''cd space tilda''' to go to the '''home''' directory.
+
|  | Enter the command '''cd ''' to go to the '''home''' directory.
  
 
|-
 
|-
 
|  | Type '''whereis gromacs''' and press ‘’’Enter’’’.  
 
|  | Type '''whereis gromacs''' and press ‘’’Enter’’’.  
 
to check if files are in /usr/local/gromcs/ directory.
 
to check if files are in /usr/local/gromcs/ directory.
−
|  |Please list the files andusing the command as seen here.
+
|  | Gromacs may get installed in'''usr local gromacs''' directory.
−
 
+
−
Gromacs may get installed in'''usr local gromacs''' directory.
+
  
 
Check if it is in this directory for you.
 
Check if it is in this directory for you.
 +
 +
Please list the files and using the command as seen here.
  
 
|-
 
|-
Line 403: Line 403:
  
 
|-
 
|-
−
|  |Type'''vim .bashrc''' and press the'''Enter'''.
+
|  |Type '''vim .bashrc''' and press the'''Enter'''.
 
|  | Let’s edit the '''dot bashrc''' file with the command seen here.
 
|  | Let’s edit the '''dot bashrc''' file with the command seen here.
  
Line 415: Line 415:
  
 
|-
 
|-
−
|  |Use the arrow key and press'''Enter''' to start a new line.
+
|  |Use the arrow key and press '''Enter''' to start a new line.
  
 
Type,'''alias gmx='/usr/local/gromacs/bin/gmx''''  
 
Type,'''alias gmx='/usr/local/gromacs/bin/gmx''''  
Line 431: Line 431:
  
 
|-
 
|-
−
|  |Type''':wq''' and press'''Enter'''.
+
|  |Type ''':wq''' and press '''Enter'''.
 
|  | To save and exit, type '''colon w q''' without '''whitespace''' and press '''Enter'''.
 
|  | To save and exit, type '''colon w q''' without '''whitespace''' and press '''Enter'''.
  
Line 439: Line 439:
  
 
|-
 
|-
−
|  |Type'''gmx help grompp''' and press Enter.
+
|  |Type '''gmx help grompp''' and press Enter.
 
|  | Next, test the installation with the '''gmx help grompp''' command as seen.
 
|  | Next, test the installation with the '''gmx help grompp''' command as seen.
  

Revision as of 10:41, 16 September 2021

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/

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 .

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 theControl panel and click on Programs and Features. Scroll down theControl 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 forWindows Subsystem for Linux.

Click on Ok.

Click on Restart Windows. The system gathers the required information.

A prompt appears asking the user toRestart Windows.

Click on Restart Windows, to complete the updates.

Type Microsoft store in the search form and pressEnter. After Windows has restarts, open theMicrosoft 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 onubuntu 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 20.04LTS 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 20.04LTS. Press the Windows key, type Ubuntu 20.04LTS and notice theUbuntu app.
Open Ubuntu 20.04LTS. 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[1]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 theDownloads folder inWindows.
For you it may be different.
Type,vim INSTALL and press Enter. Typevim 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 installGromacs 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 startGromacs 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.

PressCtrl+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 withcd space bin command.
Typels and press theEnter. List the files and notice the gmx executable here.
Typecd 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 inusr 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 theEnter. 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.
Typesource .bashrc and pressEnter. 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/

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.

Contributors and Content Editors

Ranipv076, Snehalathak

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