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

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'''System and Software Requirement'''
 
'''System and Software Requirement'''
 
|  | * 64-bit architecture and 4GB RAM or higher are must for the installation
 
|  | * 64-bit architecture and 4GB RAM or higher are must for the installation
−
* All the '''Windows''' OS updates completed
+
* All the '''Windows''' OS updates must be completed
 
* Sufficient disk space must be available for software build
 
* Sufficient disk space must be available for software build
  
 
|-
 
|-
−
|  | '''Slide Number6'''
+
|  | '''Slide Number 6'''
  
 
'''Pre-requisites'''
 
'''Pre-requisites'''
Line 137: Line 137:
 
|-
 
|-
 
|  |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''' 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.
+
|  |In the search form, type '''microsoft store''' and open it.
  
 
The '''microsoft store''' window opens.  
 
The '''microsoft store''' window opens.  
Line 156: Line 156:
  
 
|-
 
|-
−
|  |Scroll down and click on blue coloured '''Get button.'''
+
|  |Scroll down and click on blue colored '''Get button.'''
  
 
If prompted, click on '''No, Thanks'''.
 
If prompted, click on '''No, Thanks'''.
Line 166: Line 166:
 
|  |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.
  
 
|-
 
|-
Line 254: Line 256:
 
This will install the programs and libraries essential for subsequent steps.
 
This will install the programs and libraries essential for subsequent steps.
  
−
Enter the sudo user password if prompted.  
+
Enter the '''sudo''' password if prompted.  
  
 
|-
 
|-
−
|  |  
+
|  | Show installation of library messages seen on the screen.
 
|  | Allow the process to be completed.
 
|  | Allow the process to be completed.
  
Line 293: Line 295:
  
 
|-
 
|-
−
|  |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.
  
−
Let’s change the path to the newly created directory as seen here.
+
Let’s change the path to the newly created directory with the '''cd''' command.
  
 
|-
 
|-
 
|  |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'''.
  
−
|-
+
For you it may be different.
−
|  |
+
−
|  | For you it may be different.
+
  
 
|-
 
|-
−
|  |Type,'''vim INSTALL ''' and press '''Enter'''.
+
|  |Type, '''vim INSTALL ''' and press '''Enter'''.
−
|  |Type'''vim space INSTALL '''to open the file in '''vim''' text editor.
+
|  |Type '''vim space INSTALL ''' to open the file in '''vim''' text editor.
  
 
|-
 
|-
Line 314: Line 314:
 
|  | Scroll down the file using page down or down arrow key.  
 
|  | Scroll down the file using page down or down arrow key.  
  
−
Detailed stepwise commands to install'''Gromacs''' is given here.
+
Detailed step-wise commands to install '''Gromacs''' is given here.
  
 
|-
 
|-
Line 328: Line 328:
 
|-
 
|-
 
|  | Type, '''cd build''' and press '''Enter'''.
 
|  | Type, '''cd build''' and press '''Enter'''.
−
|  | Change the path to the newly created '''build '''directory as seen here.
+
|  | Change the path to the newly created '''build ''' directory as seen here.
  
 
|-
 
|-
 
|  | Type '''sudo cmake .. -DGMX_BUILD_OWN_FFTW=ON '''and press '''Enter'''.
 
|  | Type '''sudo cmake .. -DGMX_BUILD_OWN_FFTW=ON '''and press '''Enter'''.
−
|  |To start'''Gromacs build''', enter the command as seen here.
+
|  |To start '''Gromacs build''', enter the command as seen here.
  
 
|-
 
|-
Line 353: Line 353:
  
 
|-
 
|-
−
|  |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.
  
Line 364: Line 364:
 
|  | With this step the installation process for '''gromacs''' is completed.
 
|  | With this step the installation process for '''gromacs''' is completed.
  
−
I will clear the screen for clarity in the video.
+
I will clear the screen again for clarity in the video.
  
 
|-
 
|-
Line 379: Line 379:
 
|-
 
|-
 
|  |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.
  
 
|-
 
|-
−
|  |Type'''ls''' and press the'''Enter'''.
+
|  |Type '''ls''' and press the '''Enter''' key.
 
|  | List the files and notice the '''gmx''' executable here.
 
|  | List the files and notice the '''gmx''' executable here.
  
Line 392: Line 392:
 
|  | 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.
−
|  | Gromacs may get installed in'''usr local gromacs''' directory.
+
|  | Note down the path of installation using the command as seen here.
 +
 
 +
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.
 
−
 
−
|-
 
−
|  |
 
−
|  | Note down the path of installation.
 
  
 
|-
 
|-
Line 423: Line 419:
  
 
|-
 
|-
−
|  |  
+
|  | Cursor on the alias line.
−
|  | Learners must enter the path of the gmx file.  
+
|  | Learners must enter the path of the '''gmx''' file.  
  
 
|-
 
|-
Line 446: Line 442:
 
|  | I don’t see any errors in the output.  
 
|  | I don’t see any errors in the output.  
  
−
This shows, we have installed '''Gromacs'''.
+
This shows, that we have installed '''Gromacs'''.
  
 
|-
 
|-
Line 456: Line 452:
 
* Issue the following commands in the '''terminal''' after '''Ubuntu app''' installation.
 
* Issue the following commands in the '''terminal''' after '''Ubuntu app''' installation.
 
* Enter the command, '''sudo apt-get update'''
 
* Enter the command, '''sudo apt-get update'''
 +
* Enter the user '''sudo''' password if prompted
  
 
|-
 
|-
Line 461: Line 458:
  
 
'''Alternate installation method'''
 
'''Alternate installation method'''
−
|  | * Enter the user '''sudo''' password if prompted
+
|  | * Enter the command, '''sudo apt-get upgrade'''
−
* Enter the command, '''sudo apt-get upgrade'''
+
 
* Then, enter the command, '''sudo apt-get install gromacs'''
 
* Then, enter the command, '''sudo apt-get install gromacs'''
  
Line 470: Line 466:
 
'''Software Version'''
 
'''Software Version'''
 
|  | * The latest version of the software may not get installed with this method
 
|  | * The latest version of the software may not get installed with this method
−
* The version with the '''linux''' repository will get installed
+
* The version with the '''Linux''' repository will get installed
  
 
|-
 
|-

Latest revision as of 17:05, 20 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 must be completed
  • Sufficient disk space must be available for software build
Slide Number 6

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 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 pressEnter. After Windows restarts, open the Microsoft store.
Type microsoft store in the search form. In the search form, type microsoft store and open it.

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 colored 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 theUbuntu 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 password if prompted.

Show installation of library messages seen on the screen. 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 with the cd command.

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 step-wise 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 again 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 key. 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.

Note down the path of installation using the command as seen here.

Gromacs may get installed inusr local gromacs directory.

Check if it is in this directory for you.

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.

Cursor on the alias line. 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, that 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
  • Enter the user sudo password if prompted
Slide Number 9

Alternate installation method

* 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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